[2022-11-11T10:22:07+0100] [MainThread] [I] [cwltool] Resolved '/project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/download_and_run_bf_remove.cwl' to 'file:///project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/download_and_run_bf_remove.cwl' [2022-11-11T10:22:21+0100] [MainThread] [I] [toil.job] Saving graph of 2 jobs, 2 new [2022-11-11T10:22:21+0100] [MainThread] [I] [toil.job] Processing job 'ResolveIndirect' kind-ResolveIndirect/instance-mw70341g v0 [2022-11-11T10:22:21+0100] [MainThread] [I] [toil.job] Processing job 'CWLWorkflow' kind-CWLWorkflow/instance-w_wuyy5y v0 [2022-11-11T10:22:21+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T10:22:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4211/worker_log.txt [2022-11-11T10:22:23+0100] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T10:22:23+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/8279/worker_log.txt [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.0.fetchdata kind-CWLJob/instance-fgojui8c v1 with job batch system ID: 2 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.14.fetchdata kind-CWLJob/instance-uilaagfs v1 with job batch system ID: 3 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.5.fetchdata kind-CWLJob/instance-x51ergml v1 with job batch system ID: 4 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.10.fetchdata kind-CWLJob/instance-w936w8dw v1 with job batch system ID: 5 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.12.fetchdata kind-CWLJob/instance-o9ffry1c v1 with job batch system ID: 6 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.8.fetchdata kind-CWLJob/instance-cm5ui_t_ v1 with job batch system ID: 7 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.7.fetchdata kind-CWLJob/instance-q8xzvthn v1 with job batch system ID: 8 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.9.fetchdata kind-CWLJob/instance-_wbgy_0h v1 with job batch system ID: 9 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.15.fetchdata kind-CWLJob/instance-ll8x5u0c v1 with job batch system ID: 10 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.6.fetchdata kind-CWLJob/instance-01nf0eap v1 with job batch system ID: 11 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.1.fetchdata kind-CWLJob/instance-sof9oo8_ v1 with job batch system ID: 12 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.11.fetchdata kind-CWLJob/instance-o0b96byb v1 with job batch system ID: 13 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.2.fetchdata kind-CWLJob/instance-o1i3t99s v1 with job batch system ID: 14 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.13.fetchdata kind-CWLJob/instance-ip1i_ls9 v1 with job batch system ID: 15 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.16.fetchdata kind-CWLJob/instance-ntkrtamx v1 with job batch system ID: 16 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.4.fetchdata kind-CWLJob/instance-f5nfdlts v1 with job batch system ID: 17 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.3.fetchdata kind-CWLJob/instance-m1hhvypz v1 with job batch system ID: 18 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:22:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/cf5a/worker_log.txt [2022-11-11T10:22:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/eea2/worker_log.txt [2022-11-11T10:22:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4f44/worker_log.txt [2022-11-11T10:22:31+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/68c8/worker_log.txt [2022-11-11T10:22:31+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d142/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/245f/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/caa8/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/3678/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2ab3/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/10a4/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6521/worker_log.txt [2022-11-11T10:22:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0c10/worker_log.txt [2022-11-11T10:22:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d2e9/worker_log.txt [2022-11-11T10:22:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f29d/worker_log.txt [2022-11-11T10:22:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/7814/worker_log.txt [2022-11-11T10:22:34+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/3122/worker_log.txt [2022-11-11T10:22:34+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a9e8/worker_log.txt [2022-11-11T10:57:11+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/66cc/worker_log.txt [2022-11-11T10:57:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/cc77/worker_log.txt [2022-11-11T10:57:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/04fe/worker_log.txt [2022-11-11T10:57:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1da2/worker_log.txt [2022-11-11T10:57:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a0e1/worker_log.txt [2022-11-11T10:57:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/c068/worker_log.txt [2022-11-11T10:57:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0532/worker_log.txt [2022-11-11T10:57:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1a31/worker_log.txt [2022-11-11T10:57:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0dd8/worker_log.txt [2022-11-11T10:57:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/8568/worker_log.txt [2022-11-11T10:57:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5425/worker_log.txt [2022-11-11T10:57:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2cc5/worker_log.txt [2022-11-11T10:57:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/828c/worker_log.txt [2022-11-11T10:57:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6c14/worker_log.txt [2022-11-11T10:57:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1993/worker_log.txt [2022-11-11T10:57:21+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0d14/worker_log.txt [2022-11-11T10:57:21+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/b3dd/worker_log.txt [2022-11-11T10:57:21+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ae42/worker_log.txt [2022-11-11T10:57:21+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/7959/worker_log.txt [2022-11-11T10:57:28+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-mzymlv97 v1 with job batch system ID: 38 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:28+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j38n9csc v1 with job batch system ID: 39 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-gthlq2zo v1 with job batch system ID: 40 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-4vm5282q v1 with job batch system ID: 41 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-lffrw873 v1 with job batch system ID: 42 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-4n1_um9_ v1 with job batch system ID: 43 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-k17mg0jq v1 with job batch system ID: 44 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-0fpg3oyi v1 with job batch system ID: 45 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:30+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-53b40ysk v1 with job batch system ID: 46 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:30+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-ouza_5ju v1 with job batch system ID: 47 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:30+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-591wz6c_ v1 with job batch system ID: 48 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:30+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-vi_n7z1l v1 with job batch system ID: 49 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:30+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-z271dyzy v1 with job batch system ID: 50 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:30+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-p7xzw611 v1 with job batch system ID: 51 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-gy1w53up v1 with job batch system ID: 52 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-ma1m4cfu v1 with job batch system ID: 53 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-25ujhyom v1 with job batch system ID: 54 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-5y3ruutd v1 with job batch system ID: 55 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-r_5srns7 v1 with job batch system ID: 56 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-nuaeaf86 v1 with job batch system ID: 57 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-_pwvz8oh v1 with job batch system ID: 58 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-gqicn6yb v1 with job batch system ID: 59 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-1dsck2wd v1 with job batch system ID: 60 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-qixcxq9k v1 with job batch system ID: 61 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-l654cnkb v1 with job batch system ID: 62 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-3urggtla v1 with job batch system ID: 63 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:34+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-6jyyf54a v1 with job batch system ID: 64 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:34+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-t7ql5gr5 v1 with job batch system ID: 65 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:34+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-g5h1llev v1 with job batch system ID: 66 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:34+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-j5gezdb1 v1 with job batch system ID: 67 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:35+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-u9nq69n9 v1 with job batch system ID: 68 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:35+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-fowwmitq v1 with job batch system ID: 69 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v1 with job batch system ID: 70 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-g0_o0wb7 v1 with job batch system ID: 71 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:57:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4f21/worker_log.txt [2022-11-11T10:57:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0582/worker_log.txt [2022-11-11T10:57:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d458/worker_log.txt [2022-11-11T10:57:40+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/aaa5/worker_log.txt [2022-11-11T10:57:40+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4905/worker_log.txt [2022-11-11T10:57:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/cebb/worker_log.txt [2022-11-11T10:57:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0986/worker_log.txt [2022-11-11T10:57:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/b094/worker_log.txt [2022-11-11T10:57:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f8f3/worker_log.txt [2022-11-11T10:57:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/76bf/worker_log.txt [2022-11-11T10:57:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ffce/worker_log.txt [2022-11-11T10:57:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ef75/worker_log.txt [2022-11-11T10:57:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6d4c/worker_log.txt [2022-11-11T10:57:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f9dd/worker_log.txt [2022-11-11T10:57:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/3b64/worker_log.txt [2022-11-11T10:57:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/c8e4/worker_log.txt [2022-11-11T10:57:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d2be/worker_log.txt [2022-11-11T10:57:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/dde9/worker_log.txt [2022-11-11T10:57:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6463/worker_log.txt [2022-11-11T10:57:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5c7e/worker_log.txt [2022-11-11T10:57:47+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2a1c/worker_log.txt [2022-11-11T10:57:47+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d03b/worker_log.txt [2022-11-11T10:57:47+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a3c5/worker_log.txt [2022-11-11T10:57:47+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6621/worker_log.txt [2022-11-11T10:57:48+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/523e/worker_log.txt [2022-11-11T10:57:48+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/15db/worker_log.txt [2022-11-11T10:57:48+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/8ca9/worker_log.txt [2022-11-11T10:57:48+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a76d/worker_log.txt [2022-11-11T10:57:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6caa/worker_log.txt [2022-11-11T10:57:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/cfaa/worker_log.txt [2022-11-11T10:57:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6011/worker_log.txt [2022-11-11T10:57:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/73a9/worker_log.txt [2022-11-11T10:57:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/79c7/worker_log.txt [2022-11-11T10:57:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/b8f2/worker_log.txt [2022-11-11T11:22:23+0100] [MainThread] [I] [toil.leader] 17 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T12:12:08+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-uyep0b73 v1 with job batch system ID: 72 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:12:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5c49/worker_log.txt [2022-11-11T12:22:25+0100] [MainThread] [I] [toil.leader] 17 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T12:25:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-oyaldhof v1 with job batch system ID: 73 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:25:11+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5751/worker_log.txt [2022-11-11T12:25:27+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-uyep0b73 v3 with job batch system ID: 74 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:25:27+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-z271dyzy v2 with job batch system ID: 75 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:25:34+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/73e5/worker_log.txt [2022-11-11T12:25:34+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1502/worker_log.txt [2022-11-11T12:25:45+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-p7xzw611 v2 with job batch system ID: 76 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:25:52+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/3359/worker_log.txt [2022-11-11T12:26:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d161/worker_log.txt [2022-11-11T12:26:26+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/56d0/worker_log.txt [2022-11-11T12:35:32+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpl0prztp1 kind-CWLJob/instance-djmjgma8. [2022-11-11T12:35:32+0100] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v1 Exit reason: None [2022-11-11T12:35:32+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v2 [2022-11-11T12:35:32+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-djmjgma8" follows: =========> [2022-11-11T10:57:50+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T10:57:50+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T10:57:50+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v1 [2022-11-11T10:58:04+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v1) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v1 [2022-11-11T10:58:05+0100] [MainThread] [W] [cwltool] You have specified `--preserve-entire-environment` while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility. [2022-11-11T10:58:16+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T10:58:23+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpeqka6ecd$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpeqka6ecd:/tENEan \ --bind \ /tmp/tmphlp67fov:/tmp \ --bind \ /tmp/tmp2yw0yjcm/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stg01868de9-d1b7-4652-9755-df1a3c87cb2a/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /tENEan \ --net \ --network \ none \ /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \ double_tgz_elimination \ /var/lib/cwl/stg01868de9-d1b7-4652-9755-df1a3c87cb2a/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar \ LOFAR_PULSAR_ARCHIVE_locus030_L229427_red.tar WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_MEM_PER_CPU as environment variable will not be supported in the future, use APPTAINERENV_SLURM_MEM_PER_CPU instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SRUN_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_SRUN_DEBUG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODEID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODEID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASK_PID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASK_PID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CONNECTION as environment variable will not be supported in the future, use APPTAINERENV_SSH_CONNECTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PRIO_PROCESS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PRIO_PROCESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_VERBOSE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_VERBOSE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV__ as environment variable will not be supported in the future, use APPTAINERENV__ instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LANG as environment variable will not be supported in the future, use APPTAINERENV_LANG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_DIR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTCONTROL as environment variable will not be supported in the future, use APPTAINERENV_HISTCONTROL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HOSTNAME as environment variable will not be supported in the future, use APPTAINERENV_HOSTNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEPID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEPID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_DISTRIBUTION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_DISTRIBUTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_ENVIRONMENT as environment variable will not be supported in the future, use APPTAINERENV_ENVIRONMENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_KDEDIRS as environment variable will not be supported in the future, use APPTAINERENV_KDEDIRS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PROCID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PROCID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_GID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_GID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURMD_NODENAME as environment variable will not be supported in the future, use APPTAINERENV_SLURMD_NODENAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_VIRTUAL_ENV as environment variable will not be supported in the future, use APPTAINERENV_VIRTUAL_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_S_COLORS as environment variable will not be supported in the future, use APPTAINERENV_S_COLORS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_SERVICES_XML as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_SERVICES_XML instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_which_declare as environment variable will not be supported in the future, use APPTAINERENV_which_declare instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_TCP_PORT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_TCP_PORT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_SESSION_ID as environment variable will not be supported in the future, use APPTAINERENV_XDG_SESSION_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_PLUGIN as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_PLUGIN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_USER as environment variable will not be supported in the future, use APPTAINERENV_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NNODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NNODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LAUNCH_NODE_IPADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LAUNCH_NODE_IPADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_ROLE_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_ROLE_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GRID_ENV_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GRID_ENV_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PWD as environment variable will not be supported in the future, use APPTAINERENV_PWD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MYPROXY_SERVER as environment variable will not be supported in the future, use APPTAINERENV_MYPROXY_SERVER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CLUSTER_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CLUSTER_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CLIENT as environment variable will not be supported in the future, use APPTAINERENV_SSH_CLIENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_VERSION as environment variable will not be supported in the future, use APPTAINERENV_LMOD_VERSION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NTASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NTASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_UMASK as environment variable will not be supported in the future, use APPTAINERENV_SLURM_UMASK instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_LEVEL_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_LEVEL_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_ENV as environment variable will not be supported in the future, use APPTAINERENV_BASH_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SPIDER_LOGIN_UI as environment variable will not be supported in the future, use APPTAINERENV_SPIDER_LOGIN_UI instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_WORKING_CLUSTER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_WORKING_CLUSTER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SHELL_PRGM as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SHELL_PRGM instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_sys as environment variable will not be supported in the future, use APPTAINERENV_LMOD_sys instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_LCG_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOBID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOBID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CONF as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CONF instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODE_ALIASES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODE_ALIASES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_ROOT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_QOS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_QOS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR_PATTERN as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR_PATTERN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GT_PROXY_MODE as environment variable will not be supported in the future, use APPTAINERENV_GT_PROXY_MODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPUS_ON_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPUS_ON_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHELL as environment variable will not be supported in the future, use APPTAINERENV_SHELL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_UID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_UID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_X509_USER_PROXY as environment variable will not be supported in the future, use APPTAINERENV_X509_USER_PROXY instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_PARTITION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_PARTITION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_USE_CURRENT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_USE_CURRENT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_LIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_LIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_USER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NPROCS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NPROCS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHLVL as environment variable will not be supported in the future, use APPTAINERENV_SHLVL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ACCOUNT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ACCOUNT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MANPATH as environment variable will not be supported in the future, use APPTAINERENV_MANPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_CWL_SINGULARITY_CACHE as environment variable will not be supported in the future, use APPTAINERENV_CWL_SINGULARITY_CACHE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_LAUNCHER_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_LAUNCHER_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION_VAR as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION_VAR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_GTIDS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_GTIDS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LOGNAME as environment variable will not be supported in the future, use APPTAINERENV_LOGNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DBUS_SESSION_BUS_ADDRESS as environment variable will not be supported in the future, use APPTAINERENV_DBUS_SESSION_BUS_ADDRESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_RUNTIME_DIR as environment variable will not be supported in the future, use APPTAINERENV_XDG_RUNTIME_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH_ROOT as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PATH as environment variable will not be supported in the future, use APPTAINERENV_SING_USER_DEFINED_PATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_TYPE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_TYPE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DEBUGINFOD_URLS as environment variable will not be supported in the future, use APPTAINERENV_DEBUGINFOD_URLS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_TASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_TASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULESHOME as environment variable will not be supported in the future, use APPTAINERENV_MODULESHOME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SETTARG_FULL_SUPPORT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SETTARG_FULL_SUPPORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTSIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTSIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_PKG as environment variable will not be supported in the future, use APPTAINERENV_LMOD_PKG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTFILESIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTFILESIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_CMD as environment variable will not be supported in the future, use APPTAINERENV_LMOD_CMD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LOCALID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LOCALID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_GFAL_INFOSYS as environment variable will not be supported in the future, use APPTAINERENV_LCG_GFAL_INFOSYS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_OMP_NUM_THREADS as environment variable will not be supported in the future, use APPTAINERENV_OMP_NUM_THREADS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LESSOPEN as environment variable will not be supported in the future, use APPTAINERENV_LESSOPEN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_DIR as environment variable will not be supported in the future, use APPTAINERENV_LMOD_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_which%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_which%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_module%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_module%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_ml%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_ml%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PS1 as environment variable will not be supported in the future, use APPTAINERENV_PS1 instead source: /.inject-apptainer-env.sh:64:11: invalid var name Traceback (most recent call last): File "/usr/local/bin/double_tgz_elimination", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/site-packages/bf_pulp_utils/double_tgz_elimination.py", line 112, in main for ii in tar.getmembers(): File "/usr/local/lib/python3.10/tarfile.py", line 1822, in getmembers self._load() # all members, we first have to File "/usr/local/lib/python3.10/tarfile.py", line 2420, in _load tarinfo = self.next() File "/usr/local/lib/python3.10/tarfile.py", line 2342, in next self.fileobj.seek(self.offset - 1) File "/usr/local/lib/python3.10/gzip.py", line 393, in seek return self._buffer.seek(offset, whence) File "/usr/local/lib/python3.10/_compression.py", line 153, in seek data = self.read(min(io.DEFAULT_BUFFER_SIZE, offset)) File "/usr/local/lib/python3.10/gzip.py", line 507, in read raise EOFError("Compressed file ended before the " EOFError: Compressed file ended before the end-of-stream marker was reached [2022-11-11T12:17:25+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T12:35:28+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] completed permanentFail Traceback (most recent call last): File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2217, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2022-11-11T12:35:28+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T12:35:32+0100] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v2 with ID kind-CWLJob/instance-djmjgma8 to 3 [2022-11-11T12:35:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v3 with job batch system ID: 79 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:35:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/02d4/worker_log.txt [2022-11-11T12:57:07+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-jx55w_vb v1 with job batch system ID: 80 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:57:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/335a/worker_log.txt [2022-11-11T12:57:19+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-ij9t88ah v1 with job batch system ID: 81 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:57:26+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6fe9/worker_log.txt [2022-11-11T12:57:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-f_2q09d6 v1 with job batch system ID: 82 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:57:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/365e/worker_log.txt [2022-11-11T12:59:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-7ncfu44v v1 with job batch system ID: 83 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:39+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-eh_qqgfj v1 with job batch system ID: 84 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/c905/worker_log.txt [2022-11-11T12:59:43+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-7bo2hdce v1 with job batch system ID: 85 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:45+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-8gsy4gvd v1 with job batch system ID: 86 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/fbde/worker_log.txt [2022-11-11T12:59:47+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-_j3pbcl4 v1 with job batch system ID: 87 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/387b/worker_log.txt [2022-11-11T12:59:50+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-waw_03uc v1 with job batch system ID: 88 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:51+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-imys1lhz v1 with job batch system ID: 89 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T12:59:52+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ff61/worker_log.txt [2022-11-11T12:59:54+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ec12/worker_log.txt [2022-11-11T12:59:56+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1253/worker_log.txt [2022-11-11T12:59:58+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0538/worker_log.txt [2022-11-11T12:59:59+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-2sxxg0jw v1 with job batch system ID: 90 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:00:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-3n5qt9zs v1 with job batch system ID: 91 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:00:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/34bb/worker_log.txt [2022-11-11T13:00:09+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/23b8/worker_log.txt [2022-11-11T13:00:22+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-ptejspzi v1 with job batch system ID: 92 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:00:29+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/bf0a/worker_log.txt [2022-11-11T13:00:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-3r4yymdt v1 with job batch system ID: 93 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:00:35+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-buujrhai v1 with job batch system ID: 94 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:00:35+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/364a/worker_log.txt [2022-11-11T13:00:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/37b5/worker_log.txt [2022-11-11T13:13:48+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-ipw5rdmq v1 with job batch system ID: 95 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:13:55+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/e157/worker_log.txt [2022-11-11T13:14:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-oh9kuvj8 v1 with job batch system ID: 96 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:07+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-jx55w_vb v3 with job batch system ID: 97 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:07+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-591wz6c_ v2 with job batch system ID: 98 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:09+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/acce/worker_log.txt [2022-11-11T13:14:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/be62/worker_log.txt [2022-11-11T13:14:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ad40/worker_log.txt [2022-11-11T13:14:15+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-rxxpeb0s v1 with job batch system ID: 99 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:22+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-ij9t88ah v3 with job batch system ID: 100 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:22+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-j5gezdb1 v2 with job batch system ID: 101 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/e943/worker_log.txt [2022-11-11T13:14:23+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-vi_n7z1l v2 with job batch system ID: 102 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:29+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/3279/worker_log.txt [2022-11-11T13:14:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f874/worker_log.txt [2022-11-11T13:14:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1846/worker_log.txt [2022-11-11T13:14:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-f_2q09d6 v3 with job batch system ID: 103 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-qixcxq9k v2 with job batch system ID: 104 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:38+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-g5h1llev v2 with job batch system ID: 105 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/87e3/worker_log.txt [2022-11-11T13:14:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5841/worker_log.txt [2022-11-11T13:14:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/229f/worker_log.txt [2022-11-11T13:14:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/8b4c/worker_log.txt [2022-11-11T13:14:52+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-1dsck2wd v2 with job batch system ID: 107 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:14:58+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a06d/worker_log.txt [2022-11-11T13:15:00+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/8e84/worker_log.txt [2022-11-11T13:15:01+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4bb6/worker_log.txt [2022-11-11T13:15:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/6b95/worker_log.txt [2022-11-11T13:15:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ae0b/worker_log.txt [2022-11-11T13:15:26+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a40f/worker_log.txt [2022-11-11T13:16:11+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-4eao87cz v1 with job batch system ID: 113 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:13+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-2kvj92om v1 with job batch system ID: 114 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:16+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-h5iarn59 v1 with job batch system ID: 115 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f539/worker_log.txt [2022-11-11T13:16:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/cc4d/worker_log.txt [2022-11-11T13:16:19+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-t6a07d66 v1 with job batch system ID: 116 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:19+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-7htfh7cr v1 with job batch system ID: 117 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f5f4/worker_log.txt [2022-11-11T13:16:23+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-iofri_5g v1 with job batch system ID: 118 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:24+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/d70e/worker_log.txt [2022-11-11T13:16:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-fg0dbafn v1 with job batch system ID: 119 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:24+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/716c/worker_log.txt [2022-11-11T13:16:26+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-7ncfu44v v3 with job batch system ID: 120 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:26+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-k17mg0jq v2 with job batch system ID: 121 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:28+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/687f/worker_log.txt [2022-11-11T13:16:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-mzymlv97 v2 with job batch system ID: 122 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-eh_qqgfj v3 with job batch system ID: 123 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/9661/worker_log.txt [2022-11-11T13:16:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-wp3_8av9 v1 with job batch system ID: 124 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-gqicn6yb v2 with job batch system ID: 125 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-7bo2hdce v3 with job batch system ID: 126 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/72ee/worker_log.txt [2022-11-11T13:16:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/04bd/worker_log.txt [2022-11-11T13:16:34+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-02shtnmm v1 with job batch system ID: 127 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:35+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0bef/worker_log.txt [2022-11-11T13:16:35+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/7e9c/worker_log.txt [2022-11-11T13:16:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-fowwmitq v2 with job batch system ID: 128 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-8gsy4gvd v3 with job batch system ID: 129 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-_j3pbcl4 v3 with job batch system ID: 130 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-l654cnkb v2 with job batch system ID: 131 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/7c35/worker_log.txt [2022-11-11T13:16:40+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2d95/worker_log.txt [2022-11-11T13:16:40+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/fe94/worker_log.txt [2022-11-11T13:16:42+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-0fpg3oyi v2 with job batch system ID: 132 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/865e/worker_log.txt [2022-11-11T13:16:42+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-waw_03uc v3 with job batch system ID: 133 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:42+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-ma1m4cfu v2 with job batch system ID: 134 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ba81/worker_log.txt [2022-11-11T13:16:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/a4b4/worker_log.txt [2022-11-11T13:16:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4153/worker_log.txt [2022-11-11T13:16:44+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-53b40ysk v2 with job batch system ID: 135 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:44+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-imys1lhz v3 with job batch system ID: 136 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/bacd/worker_log.txt [2022-11-11T13:16:44+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j38n9csc v2 with job batch system ID: 137 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:49+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-_pwvz8oh v2 with job batch system ID: 138 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/c00b/worker_log.txt [2022-11-11T13:16:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/83a8/worker_log.txt [2022-11-11T13:16:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/85cb/worker_log.txt [2022-11-11T13:16:51+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/fa80/worker_log.txt [2022-11-11T13:16:51+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/75c6/worker_log.txt [2022-11-11T13:16:51+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2393/worker_log.txt [2022-11-11T13:16:52+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-lffrw873 v2 with job batch system ID: 139 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:52+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-2sxxg0jw v3 with job batch system ID: 140 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:52+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-u9nq69n9 v2 with job batch system ID: 141 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:52+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-3urggtla v2 with job batch system ID: 142 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:55+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-gthlq2zo v2 with job batch system ID: 143 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:55+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-3n5qt9zs v3 with job batch system ID: 144 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:56+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f1ee/worker_log.txt [2022-11-11T13:16:57+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-13asthjz v1 with job batch system ID: 145 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-gy1w53up v2 with job batch system ID: 147 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:16:59+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ea4c/worker_log.txt [2022-11-11T13:16:59+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/752c/worker_log.txt [2022-11-11T13:16:59+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/b7d8/worker_log.txt [2022-11-11T13:16:59+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/e3d4/worker_log.txt [2022-11-11T13:17:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-ouza_5ju v2 with job batch system ID: 148 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:02+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4030/worker_log.txt [2022-11-11T13:17:02+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2cf7/worker_log.txt [2022-11-11T13:17:03+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/ded2/worker_log.txt [2022-11-11T13:17:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2571/worker_log.txt [2022-11-11T13:17:04+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-a6d7zwrb v1 with job batch system ID: 151 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0541/worker_log.txt [2022-11-11T13:17:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/e3e0/worker_log.txt [2022-11-11T13:17:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/78a3/worker_log.txt [2022-11-11T13:17:06+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-4n1_um9_ v2 with job batch system ID: 152 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:09+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-4vm5282q v2 with job batch system ID: 155 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:09+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1b0b/worker_log.txt [2022-11-11T13:17:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4c14/worker_log.txt [2022-11-11T13:17:11+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-fxfve58i v1 with job batch system ID: 158 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5a32/worker_log.txt [2022-11-11T13:17:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0941/worker_log.txt [2022-11-11T13:17:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/68c6/worker_log.txt [2022-11-11T13:17:14+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-ptejspzi v3 with job batch system ID: 161 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:14+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-r_5srns7 v2 with job batch system ID: 162 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/02ff/worker_log.txt [2022-11-11T13:17:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/928d/worker_log.txt [2022-11-11T13:17:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2288/worker_log.txt [2022-11-11T13:17:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2c69/worker_log.txt [2022-11-11T13:17:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/991b/worker_log.txt [2022-11-11T13:17:19+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f2af/worker_log.txt [2022-11-11T13:17:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/34c6/worker_log.txt [2022-11-11T13:17:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/e4dc/worker_log.txt [2022-11-11T13:17:21+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-6jyyf54a v2 with job batch system ID: 167 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:21+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-3r4yymdt v3 with job batch system ID: 168 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:23+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1cd6/worker_log.txt [2022-11-11T13:17:25+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/fe09/worker_log.txt [2022-11-11T13:17:26+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/453f/worker_log.txt [2022-11-11T13:17:26+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/98df/worker_log.txt [2022-11-11T13:17:27+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/106f/worker_log.txt [2022-11-11T13:17:27+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/283f/worker_log.txt [2022-11-11T13:17:27+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-nuaeaf86 v2 with job batch system ID: 172 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:28+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/4fd2/worker_log.txt [2022-11-11T13:17:28+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-25ujhyom v2 with job batch system ID: 173 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:28+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-buujrhai v3 with job batch system ID: 174 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/5aa0/worker_log.txt [2022-11-11T13:17:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/0c48/worker_log.txt [2022-11-11T13:17:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/c459/worker_log.txt [2022-11-11T13:17:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f25f/worker_log.txt [2022-11-11T13:17:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-t7ql5gr5 v2 with job batch system ID: 176 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/179e/worker_log.txt [2022-11-11T13:17:36+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f953/worker_log.txt [2022-11-11T13:17:36+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/9e2b/worker_log.txt [2022-11-11T13:17:37+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/9933/worker_log.txt [2022-11-11T13:17:37+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-5y3ruutd v2 with job batch system ID: 179 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:17:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2ed2/worker_log.txt [2022-11-11T13:17:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/b602/worker_log.txt [2022-11-11T13:17:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/820a/worker_log.txt [2022-11-11T13:17:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/1a5f/worker_log.txt [2022-11-11T13:17:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/fbca/worker_log.txt [2022-11-11T13:17:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/f665/worker_log.txt [2022-11-11T13:17:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/77c7/worker_log.txt [2022-11-11T13:20:24+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpl0prztp1 kind-CWLJob/instance-djmjgma8. [2022-11-11T13:20:24+0100] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v3 Exit reason: None [2022-11-11T13:20:24+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v5 [2022-11-11T13:20:24+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-djmjgma8" follows: =========> [2022-11-11T12:35:39+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T12:35:39+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T12:35:39+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v4 [2022-11-11T12:35:45+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v4) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v4 [2022-11-11T12:35:45+0100] [MainThread] [W] [cwltool] You have specified `--preserve-entire-environment` while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility. [2022-11-11T12:35:50+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T12:35:53+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmp3sfvc_h0$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmp3sfvc_h0:/NDwQnl \ --bind \ /tmp/tmpnevf0g06:/tmp \ --bind \ /tmp/tmp2yw0yjcm/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stgf9ad33a3-4062-4006-b1b9-04b84ee53a08/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /NDwQnl \ --net \ --network \ none \ /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \ double_tgz_elimination \ /var/lib/cwl/stgf9ad33a3-4062-4006-b1b9-04b84ee53a08/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar \ LOFAR_PULSAR_ARCHIVE_locus030_L229427_red.tar WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_MEM_PER_CPU as environment variable will not be supported in the future, use APPTAINERENV_SLURM_MEM_PER_CPU instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SRUN_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_SRUN_DEBUG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODEID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODEID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASK_PID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASK_PID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CONNECTION as environment variable will not be supported in the future, use APPTAINERENV_SSH_CONNECTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PRIO_PROCESS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PRIO_PROCESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_VERBOSE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_VERBOSE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV__ as environment variable will not be supported in the future, use APPTAINERENV__ instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LANG as environment variable will not be supported in the future, use APPTAINERENV_LANG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_DIR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTCONTROL as environment variable will not be supported in the future, use APPTAINERENV_HISTCONTROL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HOSTNAME as environment variable will not be supported in the future, use APPTAINERENV_HOSTNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEPID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEPID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_DISTRIBUTION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_DISTRIBUTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_ENVIRONMENT as environment variable will not be supported in the future, use APPTAINERENV_ENVIRONMENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_KDEDIRS as environment variable will not be supported in the future, use APPTAINERENV_KDEDIRS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PROCID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PROCID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_GID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_GID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURMD_NODENAME as environment variable will not be supported in the future, use APPTAINERENV_SLURMD_NODENAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_VIRTUAL_ENV as environment variable will not be supported in the future, use APPTAINERENV_VIRTUAL_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_S_COLORS as environment variable will not be supported in the future, use APPTAINERENV_S_COLORS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_SERVICES_XML as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_SERVICES_XML instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_which_declare as environment variable will not be supported in the future, use APPTAINERENV_which_declare instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_TCP_PORT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_TCP_PORT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_SESSION_ID as environment variable will not be supported in the future, use APPTAINERENV_XDG_SESSION_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_PLUGIN as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_PLUGIN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_USER as environment variable will not be supported in the future, use APPTAINERENV_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NNODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NNODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LAUNCH_NODE_IPADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LAUNCH_NODE_IPADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_ROLE_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_ROLE_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GRID_ENV_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GRID_ENV_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PWD as environment variable will not be supported in the future, use APPTAINERENV_PWD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MYPROXY_SERVER as environment variable will not be supported in the future, use APPTAINERENV_MYPROXY_SERVER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CLUSTER_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CLUSTER_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CLIENT as environment variable will not be supported in the future, use APPTAINERENV_SSH_CLIENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_VERSION as environment variable will not be supported in the future, use APPTAINERENV_LMOD_VERSION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NTASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NTASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_UMASK as environment variable will not be supported in the future, use APPTAINERENV_SLURM_UMASK instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_LEVEL_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_LEVEL_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_ENV as environment variable will not be supported in the future, use APPTAINERENV_BASH_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SPIDER_LOGIN_UI as environment variable will not be supported in the future, use APPTAINERENV_SPIDER_LOGIN_UI instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_WORKING_CLUSTER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_WORKING_CLUSTER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SHELL_PRGM as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SHELL_PRGM instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_sys as environment variable will not be supported in the future, use APPTAINERENV_LMOD_sys instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_LCG_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOBID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOBID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CONF as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CONF instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODE_ALIASES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODE_ALIASES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_ROOT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_QOS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_QOS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR_PATTERN as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR_PATTERN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GT_PROXY_MODE as environment variable will not be supported in the future, use APPTAINERENV_GT_PROXY_MODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPUS_ON_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPUS_ON_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHELL as environment variable will not be supported in the future, use APPTAINERENV_SHELL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_UID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_UID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_X509_USER_PROXY as environment variable will not be supported in the future, use APPTAINERENV_X509_USER_PROXY instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_PARTITION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_PARTITION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_USE_CURRENT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_USE_CURRENT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_LIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_LIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_USER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NPROCS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NPROCS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHLVL as environment variable will not be supported in the future, use APPTAINERENV_SHLVL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ACCOUNT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ACCOUNT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MANPATH as environment variable will not be supported in the future, use APPTAINERENV_MANPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_CWL_SINGULARITY_CACHE as environment variable will not be supported in the future, use APPTAINERENV_CWL_SINGULARITY_CACHE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_LAUNCHER_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_LAUNCHER_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION_VAR as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION_VAR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_GTIDS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_GTIDS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LOGNAME as environment variable will not be supported in the future, use APPTAINERENV_LOGNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DBUS_SESSION_BUS_ADDRESS as environment variable will not be supported in the future, use APPTAINERENV_DBUS_SESSION_BUS_ADDRESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_RUNTIME_DIR as environment variable will not be supported in the future, use APPTAINERENV_XDG_RUNTIME_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH_ROOT as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PATH as environment variable will not be supported in the future, use APPTAINERENV_SING_USER_DEFINED_PATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_TYPE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_TYPE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DEBUGINFOD_URLS as environment variable will not be supported in the future, use APPTAINERENV_DEBUGINFOD_URLS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_TASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_TASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULESHOME as environment variable will not be supported in the future, use APPTAINERENV_MODULESHOME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SETTARG_FULL_SUPPORT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SETTARG_FULL_SUPPORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTSIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTSIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_PKG as environment variable will not be supported in the future, use APPTAINERENV_LMOD_PKG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTFILESIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTFILESIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_CMD as environment variable will not be supported in the future, use APPTAINERENV_LMOD_CMD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LOCALID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LOCALID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_GFAL_INFOSYS as environment variable will not be supported in the future, use APPTAINERENV_LCG_GFAL_INFOSYS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_OMP_NUM_THREADS as environment variable will not be supported in the future, use APPTAINERENV_OMP_NUM_THREADS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LESSOPEN as environment variable will not be supported in the future, use APPTAINERENV_LESSOPEN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_DIR as environment variable will not be supported in the future, use APPTAINERENV_LMOD_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_which%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_which%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_module%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_module%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_ml%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_ml%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PS1 as environment variable will not be supported in the future, use APPTAINERENV_PS1 instead source: /.inject-apptainer-env.sh:399:11: invalid var name Traceback (most recent call last): File "/usr/local/bin/double_tgz_elimination", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/site-packages/bf_pulp_utils/double_tgz_elimination.py", line 112, in main for ii in tar.getmembers(): File "/usr/local/lib/python3.10/tarfile.py", line 1822, in getmembers self._load() # all members, we first have to File "/usr/local/lib/python3.10/tarfile.py", line 2420, in _load tarinfo = self.next() File "/usr/local/lib/python3.10/tarfile.py", line 2342, in next self.fileobj.seek(self.offset - 1) File "/usr/local/lib/python3.10/gzip.py", line 393, in seek return self._buffer.seek(offset, whence) File "/usr/local/lib/python3.10/_compression.py", line 153, in seek data = self.read(min(io.DEFAULT_BUFFER_SIZE, offset)) File "/usr/local/lib/python3.10/gzip.py", line 507, in read raise EOFError("Compressed file ended before the " EOFError: Compressed file ended before the end-of-stream marker was reached [2022-11-11T13:19:34+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T13:20:24+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] completed permanentFail Traceback (most recent call last): File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2217, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2022-11-11T13:20:24+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T13:20:24+0100] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v5 with ID kind-CWLJob/instance-djmjgma8 to 2 [2022-11-11T13:20:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v6 with job batch system ID: 185 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:20:25+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/47bf/worker_log.txt [2022-11-11T13:22:27+0100] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T13:25:31+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpl0prztp1 kind-CWLJob/instance-djmjgma8. [2022-11-11T13:25:31+0100] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v6 Exit reason: None [2022-11-11T13:25:31+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v8 [2022-11-11T13:25:31+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-djmjgma8" follows: =========> [2022-11-11T13:20:25+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T13:20:25+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T13:20:25+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v7 [2022-11-11T13:20:25+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v7) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v7 [2022-11-11T13:20:25+0100] [MainThread] [W] [cwltool] You have specified `--preserve-entire-environment` while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility. [2022-11-11T13:20:26+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T13:20:26+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpl5k9x2a1$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpl5k9x2a1:/GJFlcQ \ --bind \ /tmp/tmp5fufltnl:/tmp \ --bind \ /tmp/tmp2yw0yjcm/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stgdd0a3389-4cf2-43cb-8549-ff3c07f78ffb/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /GJFlcQ \ --net \ --network \ none \ /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \ double_tgz_elimination \ /var/lib/cwl/stgdd0a3389-4cf2-43cb-8549-ff3c07f78ffb/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar \ LOFAR_PULSAR_ARCHIVE_locus030_L229427_red.tar WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_MEM_PER_CPU as environment variable will not be supported in the future, use APPTAINERENV_SLURM_MEM_PER_CPU instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SRUN_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_SRUN_DEBUG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODEID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODEID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASK_PID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASK_PID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CONNECTION as environment variable will not be supported in the future, use APPTAINERENV_SSH_CONNECTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PRIO_PROCESS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PRIO_PROCESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_VERBOSE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_VERBOSE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV__ as environment variable will not be supported in the future, use APPTAINERENV__ instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LANG as environment variable will not be supported in the future, use APPTAINERENV_LANG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_DIR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTCONTROL as environment variable will not be supported in the future, use APPTAINERENV_HISTCONTROL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HOSTNAME as environment variable will not be supported in the future, use APPTAINERENV_HOSTNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEPID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEPID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_DISTRIBUTION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_DISTRIBUTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_ENVIRONMENT as environment variable will not be supported in the future, use APPTAINERENV_ENVIRONMENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_KDEDIRS as environment variable will not be supported in the future, use APPTAINERENV_KDEDIRS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PROCID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PROCID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_GID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_GID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURMD_NODENAME as environment variable will not be supported in the future, use APPTAINERENV_SLURMD_NODENAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_VIRTUAL_ENV as environment variable will not be supported in the future, use APPTAINERENV_VIRTUAL_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_S_COLORS as environment variable will not be supported in the future, use APPTAINERENV_S_COLORS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_SERVICES_XML as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_SERVICES_XML instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_which_declare as environment variable will not be supported in the future, use APPTAINERENV_which_declare instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_TCP_PORT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_TCP_PORT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_SESSION_ID as environment variable will not be supported in the future, use APPTAINERENV_XDG_SESSION_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_PLUGIN as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_PLUGIN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_USER as environment variable will not be supported in the future, use APPTAINERENV_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NNODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NNODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LAUNCH_NODE_IPADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LAUNCH_NODE_IPADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_ROLE_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_ROLE_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GRID_ENV_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GRID_ENV_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PWD as environment variable will not be supported in the future, use APPTAINERENV_PWD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MYPROXY_SERVER as environment variable will not be supported in the future, use APPTAINERENV_MYPROXY_SERVER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CLUSTER_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CLUSTER_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CLIENT as environment variable will not be supported in the future, use APPTAINERENV_SSH_CLIENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_VERSION as environment variable will not be supported in the future, use APPTAINERENV_LMOD_VERSION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NTASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NTASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_UMASK as environment variable will not be supported in the future, use APPTAINERENV_SLURM_UMASK instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_LEVEL_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_LEVEL_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_ENV as environment variable will not be supported in the future, use APPTAINERENV_BASH_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SPIDER_LOGIN_UI as environment variable will not be supported in the future, use APPTAINERENV_SPIDER_LOGIN_UI instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_WORKING_CLUSTER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_WORKING_CLUSTER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SHELL_PRGM as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SHELL_PRGM instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_sys as environment variable will not be supported in the future, use APPTAINERENV_LMOD_sys instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_LCG_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOBID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOBID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CONF as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CONF instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODE_ALIASES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODE_ALIASES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_ROOT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_QOS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_QOS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR_PATTERN as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR_PATTERN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GT_PROXY_MODE as environment variable will not be supported in the future, use APPTAINERENV_GT_PROXY_MODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPUS_ON_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPUS_ON_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHELL as environment variable will not be supported in the future, use APPTAINERENV_SHELL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_UID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_UID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_X509_USER_PROXY as environment variable will not be supported in the future, use APPTAINERENV_X509_USER_PROXY instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_PARTITION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_PARTITION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_USE_CURRENT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_USE_CURRENT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_LIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_LIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_USER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NPROCS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NPROCS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHLVL as environment variable will not be supported in the future, use APPTAINERENV_SHLVL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ACCOUNT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ACCOUNT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MANPATH as environment variable will not be supported in the future, use APPTAINERENV_MANPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_CWL_SINGULARITY_CACHE as environment variable will not be supported in the future, use APPTAINERENV_CWL_SINGULARITY_CACHE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_LAUNCHER_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_LAUNCHER_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION_VAR as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION_VAR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_GTIDS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_GTIDS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LOGNAME as environment variable will not be supported in the future, use APPTAINERENV_LOGNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DBUS_SESSION_BUS_ADDRESS as environment variable will not be supported in the future, use APPTAINERENV_DBUS_SESSION_BUS_ADDRESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_RUNTIME_DIR as environment variable will not be supported in the future, use APPTAINERENV_XDG_RUNTIME_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH_ROOT as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PATH as environment variable will not be supported in the future, use APPTAINERENV_SING_USER_DEFINED_PATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_TYPE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_TYPE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DEBUGINFOD_URLS as environment variable will not be supported in the future, use APPTAINERENV_DEBUGINFOD_URLS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_TASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_TASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULESHOME as environment variable will not be supported in the future, use APPTAINERENV_MODULESHOME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SETTARG_FULL_SUPPORT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SETTARG_FULL_SUPPORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTSIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTSIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_PKG as environment variable will not be supported in the future, use APPTAINERENV_LMOD_PKG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTFILESIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTFILESIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_CMD as environment variable will not be supported in the future, use APPTAINERENV_LMOD_CMD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LOCALID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LOCALID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_GFAL_INFOSYS as environment variable will not be supported in the future, use APPTAINERENV_LCG_GFAL_INFOSYS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_OMP_NUM_THREADS as environment variable will not be supported in the future, use APPTAINERENV_OMP_NUM_THREADS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LESSOPEN as environment variable will not be supported in the future, use APPTAINERENV_LESSOPEN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_DIR as environment variable will not be supported in the future, use APPTAINERENV_LMOD_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_which%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_which%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_module%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_module%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_ml%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_ml%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PS1 as environment variable will not be supported in the future, use APPTAINERENV_PS1 instead source: /.inject-apptainer-env.sh:89:11: invalid var name Traceback (most recent call last): File "/usr/local/bin/double_tgz_elimination", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/site-packages/bf_pulp_utils/double_tgz_elimination.py", line 112, in main for ii in tar.getmembers(): File "/usr/local/lib/python3.10/tarfile.py", line 1822, in getmembers self._load() # all members, we first have to File "/usr/local/lib/python3.10/tarfile.py", line 2420, in _load tarinfo = self.next() File "/usr/local/lib/python3.10/tarfile.py", line 2342, in next self.fileobj.seek(self.offset - 1) File "/usr/local/lib/python3.10/gzip.py", line 393, in seek return self._buffer.seek(offset, whence) File "/usr/local/lib/python3.10/_compression.py", line 153, in seek data = self.read(min(io.DEFAULT_BUFFER_SIZE, offset)) File "/usr/local/lib/python3.10/gzip.py", line 507, in read raise EOFError("Compressed file ended before the " EOFError: Compressed file ended before the end-of-stream marker was reached [2022-11-11T13:24:42+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T13:25:31+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] completed permanentFail Traceback (most recent call last): File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2217, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2022-11-11T13:25:31+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T13:25:31+0100] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v8 with ID kind-CWLJob/instance-djmjgma8 to 1 [2022-11-11T13:25:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v9 with job batch system ID: 186 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T13:25:31+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/27be57862a71565590726471e2001f78/2971/worker_log.txt [2022-11-11T13:30:33+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpl0prztp1 kind-CWLJob/instance-djmjgma8. [2022-11-11T13:30:33+0100] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v9 Exit reason: None [2022-11-11T13:30:33+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v11 [2022-11-11T13:30:33+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-djmjgma8" follows: =========> [2022-11-11T13:25:31+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T13:25:31+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T13:25:31+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v10 [2022-11-11T13:25:32+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v10) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v10 [2022-11-11T13:25:32+0100] [MainThread] [W] [cwltool] You have specified `--preserve-entire-environment` while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility. [2022-11-11T13:25:32+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T13:25:32+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmp5nbyz09f$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmp5nbyz09f:/PuZVkV \ --bind \ /tmp/tmpej7o7rh8:/tmp \ --bind \ /tmp/tmp2yw0yjcm/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stgf780c0ab-8c54-4721-b019-21349efb746c/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /PuZVkV \ --net \ --network \ none \ /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \ double_tgz_elimination \ /var/lib/cwl/stgf780c0ab-8c54-4721-b019-21349efb746c/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar \ LOFAR_PULSAR_ARCHIVE_locus030_L229427_red.tar WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_MEM_PER_CPU as environment variable will not be supported in the future, use APPTAINERENV_SLURM_MEM_PER_CPU instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SRUN_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_SRUN_DEBUG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODEID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODEID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASK_PID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASK_PID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CONNECTION as environment variable will not be supported in the future, use APPTAINERENV_SSH_CONNECTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PRIO_PROCESS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PRIO_PROCESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_VERBOSE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_VERBOSE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV__ as environment variable will not be supported in the future, use APPTAINERENV__ instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LANG as environment variable will not be supported in the future, use APPTAINERENV_LANG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_DIR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTCONTROL as environment variable will not be supported in the future, use APPTAINERENV_HISTCONTROL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HOSTNAME as environment variable will not be supported in the future, use APPTAINERENV_HOSTNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEPID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEPID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_DISTRIBUTION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_DISTRIBUTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_ENVIRONMENT as environment variable will not be supported in the future, use APPTAINERENV_ENVIRONMENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_KDEDIRS as environment variable will not be supported in the future, use APPTAINERENV_KDEDIRS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PROCID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PROCID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_GID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_GID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURMD_NODENAME as environment variable will not be supported in the future, use APPTAINERENV_SLURMD_NODENAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_VIRTUAL_ENV as environment variable will not be supported in the future, use APPTAINERENV_VIRTUAL_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_S_COLORS as environment variable will not be supported in the future, use APPTAINERENV_S_COLORS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_SERVICES_XML as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_SERVICES_XML instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_which_declare as environment variable will not be supported in the future, use APPTAINERENV_which_declare instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_TCP_PORT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_TCP_PORT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_SESSION_ID as environment variable will not be supported in the future, use APPTAINERENV_XDG_SESSION_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_PLUGIN as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_PLUGIN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_USER as environment variable will not be supported in the future, use APPTAINERENV_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NNODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NNODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LAUNCH_NODE_IPADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LAUNCH_NODE_IPADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_ROLE_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_ROLE_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GRID_ENV_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GRID_ENV_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PWD as environment variable will not be supported in the future, use APPTAINERENV_PWD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MYPROXY_SERVER as environment variable will not be supported in the future, use APPTAINERENV_MYPROXY_SERVER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CLUSTER_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CLUSTER_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CLIENT as environment variable will not be supported in the future, use APPTAINERENV_SSH_CLIENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_VERSION as environment variable will not be supported in the future, use APPTAINERENV_LMOD_VERSION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NTASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NTASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_UMASK as environment variable will not be supported in the future, use APPTAINERENV_SLURM_UMASK instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_LEVEL_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_LEVEL_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_ENV as environment variable will not be supported in the future, use APPTAINERENV_BASH_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SPIDER_LOGIN_UI as environment variable will not be supported in the future, use APPTAINERENV_SPIDER_LOGIN_UI instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_WORKING_CLUSTER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_WORKING_CLUSTER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SHELL_PRGM as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SHELL_PRGM instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_sys as environment variable will not be supported in the future, use APPTAINERENV_LMOD_sys instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_LCG_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOBID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOBID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CONF as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CONF instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODE_ALIASES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODE_ALIASES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_ROOT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_QOS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_QOS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR_PATTERN as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR_PATTERN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GT_PROXY_MODE as environment variable will not be supported in the future, use APPTAINERENV_GT_PROXY_MODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPUS_ON_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPUS_ON_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHELL as environment variable will not be supported in the future, use APPTAINERENV_SHELL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_UID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_UID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_X509_USER_PROXY as environment variable will not be supported in the future, use APPTAINERENV_X509_USER_PROXY instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_PARTITION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_PARTITION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_USE_CURRENT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_USE_CURRENT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_LIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_LIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_USER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NPROCS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NPROCS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHLVL as environment variable will not be supported in the future, use APPTAINERENV_SHLVL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ACCOUNT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ACCOUNT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MANPATH as environment variable will not be supported in the future, use APPTAINERENV_MANPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_CWL_SINGULARITY_CACHE as environment variable will not be supported in the future, use APPTAINERENV_CWL_SINGULARITY_CACHE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_LAUNCHER_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_LAUNCHER_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION_VAR as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION_VAR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_GTIDS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_GTIDS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LOGNAME as environment variable will not be supported in the future, use APPTAINERENV_LOGNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DBUS_SESSION_BUS_ADDRESS as environment variable will not be supported in the future, use APPTAINERENV_DBUS_SESSION_BUS_ADDRESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_RUNTIME_DIR as environment variable will not be supported in the future, use APPTAINERENV_XDG_RUNTIME_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH_ROOT as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PATH as environment variable will not be supported in the future, use APPTAINERENV_SING_USER_DEFINED_PATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_TYPE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_TYPE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DEBUGINFOD_URLS as environment variable will not be supported in the future, use APPTAINERENV_DEBUGINFOD_URLS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_TASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_TASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULESHOME as environment variable will not be supported in the future, use APPTAINERENV_MODULESHOME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SETTARG_FULL_SUPPORT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SETTARG_FULL_SUPPORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTSIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTSIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_PKG as environment variable will not be supported in the future, use APPTAINERENV_LMOD_PKG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTFILESIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTFILESIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_CMD as environment variable will not be supported in the future, use APPTAINERENV_LMOD_CMD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LOCALID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LOCALID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_GFAL_INFOSYS as environment variable will not be supported in the future, use APPTAINERENV_LCG_GFAL_INFOSYS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_OMP_NUM_THREADS as environment variable will not be supported in the future, use APPTAINERENV_OMP_NUM_THREADS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LESSOPEN as environment variable will not be supported in the future, use APPTAINERENV_LESSOPEN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_DIR as environment variable will not be supported in the future, use APPTAINERENV_LMOD_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_which%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_which%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_module%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_module%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_ml%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_ml%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PS1 as environment variable will not be supported in the future, use APPTAINERENV_PS1 instead source: /.inject-apptainer-env.sh:129:11: invalid var name Traceback (most recent call last): File "/usr/local/bin/double_tgz_elimination", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/site-packages/bf_pulp_utils/double_tgz_elimination.py", line 112, in main for ii in tar.getmembers(): File "/usr/local/lib/python3.10/tarfile.py", line 1822, in getmembers self._load() # all members, we first have to File "/usr/local/lib/python3.10/tarfile.py", line 2420, in _load tarinfo = self.next() File "/usr/local/lib/python3.10/tarfile.py", line 2342, in next self.fileobj.seek(self.offset - 1) File "/usr/local/lib/python3.10/gzip.py", line 393, in seek return self._buffer.seek(offset, whence) File "/usr/local/lib/python3.10/_compression.py", line 153, in seek data = self.read(min(io.DEFAULT_BUFFER_SIZE, offset)) File "/usr/local/lib/python3.10/gzip.py", line 507, in read raise EOFError("Compressed file ended before the " EOFError: Compressed file ended before the end-of-stream marker was reached [2022-11-11T13:29:45+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T13:30:33+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] completed permanentFail Traceback (most recent call last): File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2217, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2022-11-11T13:30:33+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T13:30:33+0100] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v11 with ID kind-CWLJob/instance-djmjgma8 to 0 [2022-11-11T13:30:33+0100] [MainThread] [W] [toil.leader] Job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v12 is completely failed [2022-11-11T13:30:49+0100] [MainThread] [I] [toil.leader] Finished toil run with 7 failed jobs. [2022-11-11T13:30:49+0100] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v12 'CWLWorkflow' kind-CWLWorkflow/instance-w_wuyy5y v2 'CWLScatter' kind-CWLScatter/instance-b0pu8hk6 v3 'CWLScatter' kind-CWLScatter/instance-63zdwdnd v2 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-g0_o0wb7 v2 'CWLGather' kind-CWLGather/instance-1rvnnlsr v3 'CWLWorkflow' kind-CWLWorkflow/instance-p8wihc95 v2 [2022-11-11T13:30:49+0100] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpl0prztp1) Traceback (most recent call last): File "/project/ldv/Software/executor-venv/bin/toil-cwl-runner", line 8, in sys.exit(main()) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 3654, in main outobj = toil.start(wf1) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/common.py", line 966, in start return self._runMainLoop(rootJobDescription) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/common.py", line 1386, in _runMainLoop return Leader(config=self.config, File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/leader.py", line 309, in run raise FailedJobsException(self.jobStore, failed_jobs, exit_code=self.recommended_fail_exit_code) toil.leader.FailedJobsException: The job store '/tmp/tmpl0prztp1' contains 7 failed jobs: 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v12, 'CWLWorkflow' kind-CWLWorkflow/instance-w_wuyy5y v2, 'CWLScatter' kind-CWLScatter/instance-b0pu8hk6 v3, 'CWLScatter' kind-CWLScatter/instance-63zdwdnd v2, 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-g0_o0wb7 v2, 'CWLGather' kind-CWLGather/instance-1rvnnlsr v3, 'CWLWorkflow' kind-CWLWorkflow/instance-p8wihc95 v2 Log from job "'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v12" follows: =========> [2022-11-11T13:25:31+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T13:25:31+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T13:25:31+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v10 [2022-11-11T13:25:32+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v10) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-djmjgma8 v10 [2022-11-11T13:25:32+0100] [MainThread] [W] [cwltool] You have specified `--preserve-entire-environment` while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility. [2022-11-11T13:25:32+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T13:25:32+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmp5nbyz09f$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmp5nbyz09f:/PuZVkV \ --bind \ /tmp/tmpej7o7rh8:/tmp \ --bind \ /tmp/tmp2yw0yjcm/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stgf780c0ab-8c54-4721-b019-21349efb746c/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /PuZVkV \ --net \ --network \ none \ /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \ double_tgz_elimination \ /var/lib/cwl/stgf780c0ab-8c54-4721-b019-21349efb746c/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar \ LOFAR_PULSAR_ARCHIVE_locus030_L229427_red.tar WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_MEM_PER_CPU as environment variable will not be supported in the future, use APPTAINERENV_SLURM_MEM_PER_CPU instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SRUN_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_SRUN_DEBUG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODEID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODEID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASK_PID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASK_PID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CONNECTION as environment variable will not be supported in the future, use APPTAINERENV_SSH_CONNECTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PRIO_PROCESS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PRIO_PROCESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_VERBOSE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_VERBOSE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV__ as environment variable will not be supported in the future, use APPTAINERENV__ instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LANG as environment variable will not be supported in the future, use APPTAINERENV_LANG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_DIR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTCONTROL as environment variable will not be supported in the future, use APPTAINERENV_HISTCONTROL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HOSTNAME as environment variable will not be supported in the future, use APPTAINERENV_HOSTNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEPID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEPID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_DISTRIBUTION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_DISTRIBUTION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_ENVIRONMENT as environment variable will not be supported in the future, use APPTAINERENV_ENVIRONMENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_KDEDIRS as environment variable will not be supported in the future, use APPTAINERENV_KDEDIRS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_PROCID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_PROCID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_GID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_GID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURMD_NODENAME as environment variable will not be supported in the future, use APPTAINERENV_SLURMD_NODENAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_VIRTUAL_ENV as environment variable will not be supported in the future, use APPTAINERENV_VIRTUAL_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_S_COLORS as environment variable will not be supported in the future, use APPTAINERENV_S_COLORS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_SERVICES_XML as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_SERVICES_XML instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_which_declare as environment variable will not be supported in the future, use APPTAINERENV_which_declare instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_TCP_PORT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_TCP_PORT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_SESSION_ID as environment variable will not be supported in the future, use APPTAINERENV_XDG_SESSION_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_SD_PLUGIN as environment variable will not be supported in the future, use APPTAINERENV_GLITE_SD_PLUGIN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_USER as environment variable will not be supported in the future, use APPTAINERENV_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NNODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NNODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LAUNCH_NODE_IPADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LAUNCH_NODE_IPADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_TASKS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_TASKS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_ROLE_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_ROLE_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GRID_ENV_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GRID_ENV_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PWD as environment variable will not be supported in the future, use APPTAINERENV_PWD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MYPROXY_SERVER as environment variable will not be supported in the future, use APPTAINERENV_MYPROXY_SERVER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CLUSTER_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CLUSTER_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SSH_CLIENT as environment variable will not be supported in the future, use APPTAINERENV_SSH_CLIENT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_VERSION as environment variable will not be supported in the future, use APPTAINERENV_LMOD_VERSION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NTASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NTASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_UMASK as environment variable will not be supported in the future, use APPTAINERENV_SLURM_UMASK instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_LEVEL_REQUESTED as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_LEVEL_REQUESTED instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_ENV as environment variable will not be supported in the future, use APPTAINERENV_BASH_ENV instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SPIDER_LOGIN_UI as environment variable will not be supported in the future, use APPTAINERENV_SPIDER_LOGIN_UI instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_WORKING_CLUSTER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_WORKING_CLUSTER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SHELL_PRGM as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SHELL_PRGM instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NODELIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NODELIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NAME as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SRUN_COMM_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SRUN_COMM_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_sys as environment variable will not be supported in the future, use APPTAINERENV_LMOD_sys instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_LCG_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOBID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOBID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CONF as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CONF instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NODE_ALIASES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NODE_ALIASES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_ROOT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_QOS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_QOS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_TOPOLOGY_ADDR_PATTERN as environment variable will not be supported in the future, use APPTAINERENV_SLURM_TOPOLOGY_ADDR_PATTERN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GT_PROXY_MODE as environment variable will not be supported in the future, use APPTAINERENV_GT_PROXY_MODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPUS_ON_NODE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPUS_ON_NODE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHELL as environment variable will not be supported in the future, use APPTAINERENV_SHELL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_UID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_UID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_X509_USER_PROXY as environment variable will not be supported in the future, use APPTAINERENV_X509_USER_PROXY instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_PARTITION as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_PARTITION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SELINUX_USE_CURRENT_RANGE as environment variable will not be supported in the future, use APPTAINERENV_SELINUX_USE_CURRENT_RANGE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_LIST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_LIST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL as environment variable will not be supported in the future, use APPTAINERENV_GLOBUS_GSSAPI_MAX_TLS_PROTOCOL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_USER as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_USER instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_NPROCS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_NPROCS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SHLVL as environment variable will not be supported in the future, use APPTAINERENV_SHLVL instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_SUBMIT_HOST as environment variable will not be supported in the future, use APPTAINERENV_SLURM_SUBMIT_HOST instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ACCOUNT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ACCOUNT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MANPATH as environment variable will not be supported in the future, use APPTAINERENV_MANPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_CWL_SINGULARITY_CACHE as environment variable will not be supported in the future, use APPTAINERENV_CWL_SINGULARITY_CACHE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_LAUNCHER_PORT as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_LAUNCHER_PORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION_VAR as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION_VAR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_GTIDS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_GTIDS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LOGNAME as environment variable will not be supported in the future, use APPTAINERENV_LOGNAME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DBUS_SESSION_BUS_ADDRESS as environment variable will not be supported in the future, use APPTAINERENV_DBUS_SESSION_BUS_ADDRESS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_XDG_RUNTIME_DIR as environment variable will not be supported in the future, use APPTAINERENV_XDG_RUNTIME_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_GLITE_LOCATION as environment variable will not be supported in the future, use APPTAINERENV_GLITE_LOCATION instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULEPATH_ROOT as environment variable will not be supported in the future, use APPTAINERENV_MODULEPATH_ROOT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PATH as environment variable will not be supported in the future, use APPTAINERENV_SING_USER_DEFINED_PATH instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_ID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_ID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_CPU_BIND_TYPE as environment variable will not be supported in the future, use APPTAINERENV_SLURM_CPU_BIND_TYPE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_DEBUGINFOD_URLS as environment variable will not be supported in the future, use APPTAINERENV_DEBUGINFOD_URLS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_TASKS as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_TASKS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_MODULESHOME as environment variable will not be supported in the future, use APPTAINERENV_MODULESHOME instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_SETTARG_FULL_SUPPORT as environment variable will not be supported in the future, use APPTAINERENV_LMOD_SETTARG_FULL_SUPPORT instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTSIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTSIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 as environment variable will not be supported in the future, use APPTAINERENV_SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0 instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_PKG as environment variable will not be supported in the future, use APPTAINERENV_LMOD_PKG instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_HISTFILESIZE as environment variable will not be supported in the future, use APPTAINERENV_HISTFILESIZE instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_STEP_NUM_NODES as environment variable will not be supported in the future, use APPTAINERENV_SLURM_STEP_NUM_NODES instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_CMD as environment variable will not be supported in the future, use APPTAINERENV_LMOD_CMD instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_SLURM_LOCALID as environment variable will not be supported in the future, use APPTAINERENV_SLURM_LOCALID instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LCG_GFAL_INFOSYS as environment variable will not be supported in the future, use APPTAINERENV_LCG_GFAL_INFOSYS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_OMP_NUM_THREADS as environment variable will not be supported in the future, use APPTAINERENV_OMP_NUM_THREADS instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LESSOPEN as environment variable will not be supported in the future, use APPTAINERENV_LESSOPEN instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LMOD_DIR as environment variable will not be supported in the future, use APPTAINERENV_LMOD_DIR instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_which%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_which%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_module%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_module%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_BASH_FUNC_ml%% as environment variable will not be supported in the future, use APPTAINERENV_BASH_FUNC_ml%% instead WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_PS1 as environment variable will not be supported in the future, use APPTAINERENV_PS1 instead source: /.inject-apptainer-env.sh:129:11: invalid var name Traceback (most recent call last): File "/usr/local/bin/double_tgz_elimination", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/site-packages/bf_pulp_utils/double_tgz_elimination.py", line 112, in main for ii in tar.getmembers(): File "/usr/local/lib/python3.10/tarfile.py", line 1822, in getmembers self._load() # all members, we first have to File "/usr/local/lib/python3.10/tarfile.py", line 2420, in _load tarinfo = self.next() File "/usr/local/lib/python3.10/tarfile.py", line 2342, in next self.fileobj.seek(self.offset - 1) File "/usr/local/lib/python3.10/gzip.py", line 393, in seek return self._buffer.seek(offset, whence) File "/usr/local/lib/python3.10/_compression.py", line 153, in seek data = self.read(min(io.DEFAULT_BUFFER_SIZE, offset)) File "/usr/local/lib/python3.10/gzip.py", line 507, in read raise EOFError("Compressed file ended before the " EOFError: Compressed file ended before the end-of-stream marker was reached [2022-11-11T13:29:45+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T13:30:33+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] completed permanentFail Traceback (most recent call last): File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/project/ldv/Software/executor-venv/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2217, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2022-11-11T13:30:33+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= srun: error: wn-hb-03: task 0: Exited with exit code 1