[2022-11-11T07:05:41+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' [2022-11-11T07:05:55+0100] [MainThread] [I] [toil.job] Saving graph of 2 jobs, 2 new [2022-11-11T07:05:55+0100] [MainThread] [I] [toil.job] Processing job 'ResolveIndirect' kind-ResolveIndirect/instance-6u_2i3u9 v0 [2022-11-11T07:05:55+0100] [MainThread] [I] [toil.job] Processing job 'CWLWorkflow' kind-CWLWorkflow/instance-jlxu1qh5 v0 [2022-11-11T07:05:55+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T07:05:56+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/bc95/worker_log.txt [2022-11-11T07:05:57+0100] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T07:05:57+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f5d5/worker_log.txt [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.15.fetchdata kind-CWLJob/instance-fr6zcnqw v1 with job batch system ID: 2 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.0.fetchdata kind-CWLJob/instance-1g8tarmc v1 with job batch system ID: 3 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.9.fetchdata kind-CWLJob/instance-jxzxivkc v1 with job batch system ID: 4 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.10.fetchdata kind-CWLJob/instance-0iyfk6eu v1 with job batch system ID: 5 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.6.fetchdata kind-CWLJob/instance-nd9fkph5 v1 with job batch system ID: 6 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.7.fetchdata kind-CWLJob/instance-odxy7pj9 v1 with job batch system ID: 7 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.1.fetchdata kind-CWLJob/instance-xcn4t9p1 v1 with job batch system ID: 8 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.12.fetchdata kind-CWLJob/instance-nfqnb7ob v1 with job batch system ID: 9 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.8.fetchdata kind-CWLJob/instance-51xzxgs3 v1 with job batch system ID: 10 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.14.fetchdata kind-CWLJob/instance-h686rybz v1 with job batch system ID: 11 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.11.fetchdata kind-CWLJob/instance-_c5m0c6k v1 with job batch system ID: 12 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.13.fetchdata kind-CWLJob/instance-wx3wcl5g v1 with job batch system ID: 13 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.2.fetchdata kind-CWLJob/instance-cxvk1n1w v1 with job batch system ID: 14 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.4.fetchdata kind-CWLJob/instance-16nen5r8 v1 with job batch system ID: 15 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.16.fetchdata kind-CWLJob/instance-e44svjl9 v1 with job batch system ID: 16 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.3.fetchdata kind-CWLJob/instance-oigk8le6 v1 with job batch system ID: 17 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:05:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_bf_remove.cwl.5.fetchdata kind-CWLJob/instance-xhtgw96p v1 with job batch system ID: 18 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:06:02+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/16d6/worker_log.txt [2022-11-11T07:06:03+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/dd4d/worker_log.txt [2022-11-11T07:06:03+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/d979/worker_log.txt [2022-11-11T07:06:03+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cac9/worker_log.txt [2022-11-11T07:06:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c74a/worker_log.txt [2022-11-11T07:06:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4416/worker_log.txt [2022-11-11T07:06:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/027a/worker_log.txt [2022-11-11T07:06:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/059e/worker_log.txt [2022-11-11T07:06:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f834/worker_log.txt [2022-11-11T07:06:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ab8d/worker_log.txt [2022-11-11T07:06:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/fb06/worker_log.txt [2022-11-11T07:06:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f55c/worker_log.txt [2022-11-11T07:06:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6b6f/worker_log.txt [2022-11-11T07:06:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/446d/worker_log.txt [2022-11-11T07:06:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9fbc/worker_log.txt [2022-11-11T07:06:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/d510/worker_log.txt [2022-11-11T07:06:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4244/worker_log.txt [2022-11-11T07:35:34+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4372/worker_log.txt [2022-11-11T07:35:35+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/3056/worker_log.txt [2022-11-11T07:35:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6f50/worker_log.txt [2022-11-11T07:35:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6395/worker_log.txt [2022-11-11T07:35:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/19c2/worker_log.txt [2022-11-11T07:35:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/1907/worker_log.txt [2022-11-11T07:35:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/b36a/worker_log.txt [2022-11-11T07:35:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8a55/worker_log.txt [2022-11-11T07:35:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9b0d/worker_log.txt [2022-11-11T07:35:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/931e/worker_log.txt [2022-11-11T07:35:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6e94/worker_log.txt [2022-11-11T07:35:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/aa94/worker_log.txt [2022-11-11T07:35:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9b7a/worker_log.txt [2022-11-11T07:35:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/52c2/worker_log.txt [2022-11-11T07:35:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6a5e/worker_log.txt [2022-11-11T07:35:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/aa1d/worker_log.txt [2022-11-11T07:35:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4547/worker_log.txt [2022-11-11T07:35:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/39df/worker_log.txt [2022-11-11T07:35:45+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/fb6e/worker_log.txt [2022-11-11T07:35:54+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-o6lix87v v1 with job batch system ID: 38 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:54+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-o5qqv6d3 v1 with job batch system ID: 39 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:54+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-pf7bm6ja v1 with job batch system ID: 40 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:54+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-duqmdsf8 v1 with job batch system ID: 41 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:55+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-htvaux7r v1 with job batch system ID: 42 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:55+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-o7sju6wg v1 with job batch system ID: 43 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-__z6xqdc v1 with job batch system ID: 44 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-pcn6mc9i v1 with job batch system ID: 45 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-fnn4jbsm v1 with job batch system ID: 46 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-t51tzcdh v1 with job batch system ID: 47 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-zemomvnb v1 with job batch system ID: 48 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-ecg1xc4d v1 with job batch system ID: 49 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:57+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-01js4f3w v1 with job batch system ID: 50 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:57+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-5aff46jc v1 with job batch system ID: 51 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:57+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-le8eknc4 v1 with job batch system ID: 52 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:57+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-o63las5s v1 with job batch system ID: 53 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-g4_gkitb v1 with job batch system ID: 54 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v1 with job batch system ID: 55 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-eioeajsb v1 with job batch system ID: 56 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:58+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-66zgl8ze v1 with job batch system ID: 57 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:59+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-hisemsw3 v1 with job batch system ID: 58 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:59+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-euc1tgpm v1 with job batch system ID: 59 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:59+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-y81o41ja v1 with job batch system ID: 60 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:35:59+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-25c6woq1 v1 with job batch system ID: 61 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-2etut43w v1 with job batch system ID: 62 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-yb4j22y9 v1 with job batch system ID: 63 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-3pw8pkmi v1 with job batch system ID: 64 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-c0p9vg3q v1 with job batch system ID: 65 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:01+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-6614ui53 v1 with job batch system ID: 66 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:01+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-7nk3r2ui v1 with job batch system ID: 67 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-hdsd1_9r v1 with job batch system ID: 68 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-w4c0vqj2 v1 with job batch system ID: 69 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-sc5nw7zl v1 with job batch system ID: 70 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-llvoygk9 v1 with job batch system ID: 71 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T07:36:04+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/0fbd/worker_log.txt [2022-11-11T07:36:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9ea6/worker_log.txt [2022-11-11T07:36:05+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8d59/worker_log.txt [2022-11-11T07:36:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4120/worker_log.txt [2022-11-11T07:36:06+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/e5b9/worker_log.txt [2022-11-11T07:36:07+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/29f3/worker_log.txt [2022-11-11T07:36:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ce3d/worker_log.txt [2022-11-11T07:36:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/39a3/worker_log.txt [2022-11-11T07:36:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2696/worker_log.txt [2022-11-11T07:36:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ffa6/worker_log.txt [2022-11-11T07:36:09+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c75f/worker_log.txt [2022-11-11T07:36:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4442/worker_log.txt [2022-11-11T07:36:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/281d/worker_log.txt [2022-11-11T07:36:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/21c5/worker_log.txt [2022-11-11T07:36:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/771d/worker_log.txt [2022-11-11T07:36:11+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/e5c1/worker_log.txt [2022-11-11T07:36:11+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9a67/worker_log.txt [2022-11-11T07:36:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/d48d/worker_log.txt [2022-11-11T07:36:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4b52/worker_log.txt [2022-11-11T07:36:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ba5a/worker_log.txt [2022-11-11T07:36:13+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/edc9/worker_log.txt [2022-11-11T07:36:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/87fe/worker_log.txt [2022-11-11T07:36:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ee5d/worker_log.txt [2022-11-11T07:36:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/7a0a/worker_log.txt [2022-11-11T07:36:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/0eab/worker_log.txt [2022-11-11T07:36:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/347d/worker_log.txt [2022-11-11T07:36:16+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4e2c/worker_log.txt [2022-11-11T07:36:16+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/46c3/worker_log.txt [2022-11-11T07:36:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8f4f/worker_log.txt [2022-11-11T07:36:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cd77/worker_log.txt [2022-11-11T07:36:17+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/a2b0/worker_log.txt [2022-11-11T07:36:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/92e0/worker_log.txt [2022-11-11T07:36:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/571a/worker_log.txt [2022-11-11T07:36:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ec46/worker_log.txt [2022-11-11T08:05:59+0100] [MainThread] [I] [toil.leader] 17 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T08:50:06+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-hdib83g7 v1 with job batch system ID: 72 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T08:51:03+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/69b7/worker_log.txt [2022-11-11T09:04:19+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-uh7jfboc v1 with job batch system ID: 73 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:04:27+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6186/worker_log.txt [2022-11-11T09:04:42+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-__z6xqdc v2 with job batch system ID: 74 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:04:42+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-hdib83g7 v3 with job batch system ID: 75 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:04:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/a935/worker_log.txt [2022-11-11T09:04:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/27e4/worker_log.txt [2022-11-11T09:05:02+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-pcn6mc9i v2 with job batch system ID: 76 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:05:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8fe3/worker_log.txt [2022-11-11T09:05:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/96e1/worker_log.txt [2022-11-11T09:05:59+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/3ab8/worker_log.txt [2022-11-11T09:06:00+0100] [MainThread] [I] [toil.leader] 17 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T09:16:13+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpidflinbp kind-CWLJob/instance-j7fh8axw. [2022-11-11T09:16:13+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-j7fh8axw v1 Exit reason: None [2022-11-11T09:16:13+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-j7fh8axw v2 [2022-11-11T09:16:13+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-j7fh8axw" follows: =========> [2022-11-11T07:36:12+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T07:36:12+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T07:36:12+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v1 [2022-11-11T07:36:26+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v1) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v1 [2022-11-11T07:36:26+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. [2022-11-11T07:36:39+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T07:36:47+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpcwfnqd3q$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpcwfnqd3q:/UfLjWo \ --bind \ /tmp/tmpu61rija4:/tmp \ --bind \ /tmp/tmp72qk9_cd/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stg8bc1ad62-228e-4a0b-88fe-f173ddc4942b/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /UfLjWo \ --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/stg8bc1ad62-228e-4a0b-88fe-f173ddc4942b/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 [2022-11-11T08:57:39+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T09:16:09+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 [2022-11-11T09:16:09+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T09:16:13+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-j7fh8axw v2 with ID kind-CWLJob/instance-j7fh8axw to 3 [2022-11-11T09:16:13+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v3 with job batch system ID: 79 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:16:21+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/1beb/worker_log.txt [2022-11-11T09:39:22+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-jfuluqo1 v1 with job batch system ID: 80 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:39:31+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/814a/worker_log.txt [2022-11-11T09:39:42+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-59ekqhdl v1 with job batch system ID: 81 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:39:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/bfa3/worker_log.txt [2022-11-11T09:42:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-t5ly1bf7 v1 with job batch system ID: 82 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:42:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/a2d2/worker_log.txt [2022-11-11T09:42:51+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-s3ufcsq9 v1 with job batch system ID: 83 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:42:58+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/836f/worker_log.txt [2022-11-11T09:44:20+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-j6ku7bzf v1 with job batch system ID: 84 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:27+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/91b9/worker_log.txt [2022-11-11T09:44:32+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-rj1p88tc v1 with job batch system ID: 85 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-13v5cwci v1 with job batch system ID: 86 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-6seo4ki4 v1 with job batch system ID: 87 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6eb9/worker_log.txt [2022-11-11T09:44:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6e26/worker_log.txt [2022-11-11T09:44:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8162/worker_log.txt [2022-11-11T09:44:43+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-34zd8o0h v1 with job batch system ID: 88 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:45+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-9ps5681u v1 with job batch system ID: 89 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:48+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-9gpw7ro2 v1 with job batch system ID: 90 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:44:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2374/worker_log.txt [2022-11-11T09:44:52+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/459e/worker_log.txt [2022-11-11T09:44:55+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8f6c/worker_log.txt [2022-11-11T09:45:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-k1scoja4 v1 with job batch system ID: 91 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:45:03+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-otm36zvw v1 with job batch system ID: 92 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:45:07+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/707e/worker_log.txt [2022-11-11T09:45:09+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-nhcoa62e v1 with job batch system ID: 93 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:45:09+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8168/worker_log.txt [2022-11-11T09:45:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9942/worker_log.txt [2022-11-11T09:45:15+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-ee0cdy49 v1 with job batch system ID: 94 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:45:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8507/worker_log.txt [2022-11-11T09:56:41+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-iyqs_b_k v1 with job batch system ID: 95 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:56:48+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/521d/worker_log.txt [2022-11-11T09:56:54+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-gii587ij v1 with job batch system ID: 96 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:01+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2661/worker_log.txt [2022-11-11T09:57:01+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-jfuluqo1 v3 with job batch system ID: 97 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:01+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-66zgl8ze v2 with job batch system ID: 98 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/de4e/worker_log.txt [2022-11-11T09:57:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/4ada/worker_log.txt [2022-11-11T09:57:14+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-59ekqhdl v3 with job batch system ID: 99 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:14+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-le8eknc4 v2 with job batch system ID: 100 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:18+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-eioeajsb v2 with job batch system ID: 101 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/993d/worker_log.txt [2022-11-11T09:57:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/41f0/worker_log.txt [2022-11-11T09:57:25+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f334/worker_log.txt [2022-11-11T09:57:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-o63las5s v2 with job batch system ID: 102 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:57:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8438/worker_log.txt [2022-11-11T09:57:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/5fd1/worker_log.txt [2022-11-11T09:57:53+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/bba9/worker_log.txt [2022-11-11T09:57:56+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/e46f/worker_log.txt [2022-11-11T09:58:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/94db/worker_log.txt [2022-11-11T09:59:35+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-hkotbus0 v1 with job batch system ID: 107 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:59:41+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ae54/worker_log.txt [2022-11-11T09:59:51+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-x15ke2kb v1 with job batch system ID: 108 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:59:51+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-t5ly1bf7 v3 with job batch system ID: 109 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:59:51+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-t51tzcdh v2 with job batch system ID: 110 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T09:59:57+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/e551/worker_log.txt [2022-11-11T09:59:57+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/9307/worker_log.txt [2022-11-11T09:59:57+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/7a3e/worker_log.txt [2022-11-11T10:00:05+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-fnn4jbsm v2 with job batch system ID: 111 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:00:08+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-s3ufcsq9 v3 with job batch system ID: 112 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:00:08+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-llvoygk9 v2 with job batch system ID: 113 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:00:11+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cecc/worker_log.txt [2022-11-11T10:00:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c0a6/worker_log.txt [2022-11-11T10:00:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c5ae/worker_log.txt [2022-11-11T10:00:23+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-sc5nw7zl v2 with job batch system ID: 115 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:00:25+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/31a2/worker_log.txt [2022-11-11T10:00:29+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/0f5a/worker_log.txt [2022-11-11T10:00:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8908/worker_log.txt [2022-11-11T10:00:42+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/caa0/worker_log.txt [2022-11-11T10:00:57+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6ebc/worker_log.txt [2022-11-11T10:01:07+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-1woh8iwj v1 with job batch system ID: 119 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/28b7/worker_log.txt [2022-11-11T10:01:15+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-ybrrtuip v1 with job batch system ID: 120 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:16+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-pft3slv4 v1 with job batch system ID: 121 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:20+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-a1lx095x v1 with job batch system ID: 122 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:20+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/dc15/worker_log.txt [2022-11-11T10:01:21+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-j6ku7bzf v3 with job batch system ID: 123 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:21+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-htvaux7r v2 with job batch system ID: 124 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:21+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/8622/worker_log.txt [2022-11-11T10:01:24+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-q2jaz4fm v1 with job batch system ID: 125 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:25+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/3389/worker_log.txt [2022-11-11T10:01:27+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2b02/worker_log.txt [2022-11-11T10:01:27+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/7afa/worker_log.txt [2022-11-11T10:01:28+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-yavs81dm v1 with job batch system ID: 126 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:30+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/df4e/worker_log.txt [2022-11-11T10:01:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-o5qqv6d3 v2 with job batch system ID: 127 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:31+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-rj1p88tc v3 with job batch system ID: 128 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-lqx2c17p v1 with job batch system ID: 129 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-2etut43w v2 with job batch system ID: 130 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-13v5cwci v3 with job batch system ID: 131 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:34+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/275a/worker_log.txt [2022-11-11T10:01:36+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-o7sju6wg v2 with job batch system ID: 132 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/dec0/worker_log.txt [2022-11-11T10:01:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/90e6/worker_log.txt [2022-11-11T10:01:38+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-duqmdsf8 v2 with job batch system ID: 133 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:38+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-6seo4ki4 v3 with job batch system ID: 134 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:39+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/b4b5/worker_log.txt [2022-11-11T10:01:40+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/33ad/worker_log.txt [2022-11-11T10:01:40+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-llv7xwsy v1 with job batch system ID: 135 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:40+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cc00/worker_log.txt [2022-11-11T10:01:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/1a97/worker_log.txt [2022-11-11T10:01:44+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-5aff46jc v2 with job batch system ID: 136 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:44+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-34zd8o0h v3 with job batch system ID: 137 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:45+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-vdsc2k_n v1 with job batch system ID: 138 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/1efa/worker_log.txt [2022-11-11T10:01:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/e3d4/worker_log.txt [2022-11-11T10:01:47+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-o6lix87v v2 with job batch system ID: 139 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:47+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/3f8b/worker_log.txt [2022-11-11T10:01:48+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-9ps5681u v3 with job batch system ID: 140 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:48+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-3pw8pkmi v2 with job batch system ID: 141 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:49+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-hup73el3 v1 with job batch system ID: 142 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:49+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-yb4j22y9 v2 with job batch system ID: 143 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:51+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ca7d/worker_log.txt [2022-11-11T10:01:51+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2701/worker_log.txt [2022-11-11T10:01:52+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c715/worker_log.txt [2022-11-11T10:01:53+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-9gpw7ro2 v3 with job batch system ID: 145 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:53+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-7nk3r2ui v2 with job batch system ID: 146 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:54+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c36d/worker_log.txt [2022-11-11T10:01:55+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/98e7/worker_log.txt [2022-11-11T10:01:55+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/fc78/worker_log.txt [2022-11-11T10:01:55+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c725/worker_log.txt [2022-11-11T10:01:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.format_ingest.format_ingest.cwl kind-CWLJob/instance-7iro7m3s v1 with job batch system ID: 147 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:01:56+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/03ab/worker_log.txt [2022-11-11T10:01:56+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-pf7bm6ja v2 with job batch system ID: 148 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:00+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ff4c/worker_log.txt [2022-11-11T10:02:00+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f169/worker_log.txt [2022-11-11T10:02:00+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/5a03/worker_log.txt [2022-11-11T10:02:00+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-01js4f3w v2 with job batch system ID: 149 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:01+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-k1scoja4 v3 with job batch system ID: 150 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:01+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-y81o41ja v2 with job batch system ID: 151 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:02+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/209f/worker_log.txt [2022-11-11T10:02:03+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c0c7/worker_log.txt [2022-11-11T10:02:04+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-c0p9vg3q v2 with job batch system ID: 153 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:05+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-ecg1xc4d v2 with job batch system ID: 155 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:05+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-otm36zvw v3 with job batch system ID: 156 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:07+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cfa5/worker_log.txt [2022-11-11T10:02:08+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-6614ui53 v2 with job batch system ID: 157 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/951e/worker_log.txt [2022-11-11T10:02:08+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/baab/worker_log.txt [2022-11-11T10:02:09+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-nhcoa62e v3 with job batch system ID: 159 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:09+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-w4c0vqj2 v2 with job batch system ID: 160 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:09+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/a6b2/worker_log.txt [2022-11-11T10:02:10+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f5ac/worker_log.txt [2022-11-11T10:02:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/6dff/worker_log.txt [2022-11-11T10:02:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2047/worker_log.txt [2022-11-11T10:02:12+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/917d/worker_log.txt [2022-11-11T10:02:14+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/3e98/worker_log.txt [2022-11-11T10:02:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/1e42/worker_log.txt [2022-11-11T10:02:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/32d9/worker_log.txt [2022-11-11T10:02:15+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/0788/worker_log.txt [2022-11-11T10:02:16+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-hisemsw3 v2 with job batch system ID: 163 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:16+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.compute_md5sum.computemd5.cwl kind-CWLJob/instance-ee0cdy49 v3 with job batch system ID: 164 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:17+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-25c6woq1 v2 with job batch system ID: 165 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:18+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/e07c/worker_log.txt [2022-11-11T10:02:20+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-zemomvnb v2 with job batch system ID: 169 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/0f8c/worker_log.txt [2022-11-11T10:02:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/af26/worker_log.txt [2022-11-11T10:02:22+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-hdsd1_9r v2 with job batch system ID: 171 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:22+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/84d9/worker_log.txt [2022-11-11T10:02:23+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2b8f/worker_log.txt [2022-11-11T10:02:24+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/146a/worker_log.txt [2022-11-11T10:02:24+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/1c51/worker_log.txt [2022-11-11T10:02:25+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c11a/worker_log.txt [2022-11-11T10:02:26+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/bd61/worker_log.txt [2022-11-11T10:02:28+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/d729/worker_log.txt [2022-11-11T10:02:28+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/f702/worker_log.txt [2022-11-11T10:02:29+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-euc1tgpm v2 with job batch system ID: 173 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:02:32+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/3aba/worker_log.txt [2022-11-11T10:02:37+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/a7a9/worker_log.txt [2022-11-11T10:02:37+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cbcb/worker_log.txt [2022-11-11T10:02:38+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/eec9/worker_log.txt [2022-11-11T10:02:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/71aa/worker_log.txt [2022-11-11T10:02:43+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/d66c/worker_log.txt [2022-11-11T10:02:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/ab95/worker_log.txt [2022-11-11T10:02:44+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/d5a0/worker_log.txt [2022-11-11T10:02:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/5d9e/worker_log.txt [2022-11-11T10:02:46+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/38b6/worker_log.txt [2022-11-11T10:02:49+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/2fe3/worker_log.txt [2022-11-11T10:02:50+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/cf3d/worker_log.txt [2022-11-11T10:02:51+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/c0d6/worker_log.txt [2022-11-11T10:05:53+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpidflinbp kind-CWLJob/instance-j7fh8axw. [2022-11-11T10:05:53+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-j7fh8axw v3 Exit reason: None [2022-11-11T10:05:53+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-j7fh8axw v5 [2022-11-11T10:05:53+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-j7fh8axw" follows: =========> [2022-11-11T09:16:21+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T09:16:21+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T09:16:21+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v4 [2022-11-11T09:16:28+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v4) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v4 [2022-11-11T09:16:29+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. [2022-11-11T09:16:34+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T09:16:39+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpmzchaqxe$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpmzchaqxe:/OKtWlM \ --bind \ /tmp/tmpu78vjtgs:/tmp \ --bind \ /tmp/tmp72qk9_cd/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stg3099be2c-1720-4c3b-852d-1c49045a853e/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /OKtWlM \ --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/stg3099be2c-1720-4c3b-852d-1c49045a853e/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:9:11: 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 [2022-11-11T10:04:40+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T10:05:53+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 [2022-11-11T10:05:53+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T10:05:53+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-j7fh8axw v5 with ID kind-CWLJob/instance-j7fh8axw to 2 [2022-11-11T10:05:53+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v6 with job batch system ID: 185 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:05:56+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/bcbf/worker_log.txt [2022-11-11T10:06:01+0100] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2022-11-11T10:11:33+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpidflinbp kind-CWLJob/instance-j7fh8axw. [2022-11-11T10:11:33+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-j7fh8axw v6 Exit reason: None [2022-11-11T10:11:33+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-j7fh8axw v8 [2022-11-11T10:11:33+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-j7fh8axw" follows: =========> [2022-11-11T10:05:56+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T10:05:56+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T10:05:56+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v7 [2022-11-11T10:05:56+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v7) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v7 [2022-11-11T10:05:56+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. [2022-11-11T10:05:57+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T10:05:57+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpk8wl3c2f$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpk8wl3c2f:/GlPFXB \ --bind \ /tmp/tmpxich2m74:/tmp \ --bind \ /tmp/tmp72qk9_cd/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stg8641fd25-1904-4c2f-a57e-d0345cd9b589/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /GlPFXB \ --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/stg8641fd25-1904-4c2f-a57e-d0345cd9b589/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:114:11: 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 [2022-11-11T10:10:41+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T10:11:33+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 [2022-11-11T10:11:33+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T10:11:33+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-j7fh8axw v8 with ID kind-CWLJob/instance-j7fh8axw to 1 [2022-11-11T10:11:33+0100] [MainThread] [I] [toil.leader] Issued job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v9 with job batch system ID: 186 and cores: 1, disk: 3.0 Gi, and memory: 2.0 Gi [2022-11-11T10:11:33+0100] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/ae300d3b28f755cc8803f1addcdd3692/0bf2/worker_log.txt [2022-11-11T10:16:50+0100] [Thread-9 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob file:/tmp/tmpidflinbp kind-CWLJob/instance-j7fh8axw. [2022-11-11T10:16:50+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-j7fh8axw v9 Exit reason: None [2022-11-11T10:16:50+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-j7fh8axw v11 [2022-11-11T10:16:50+0100] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-j7fh8axw" follows: =========> [2022-11-11T10:11:33+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T10:11:33+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T10:11:33+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v10 [2022-11-11T10:11:34+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v10) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v10 [2022-11-11T10:11:34+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. [2022-11-11T10:11:34+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T10:11:34+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpxh5j6pnb$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpxh5j6pnb:/DphHOM \ --bind \ /tmp/tmp7pcnleck:/tmp \ --bind \ /tmp/tmp72qk9_cd/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stgf8f4bade-64cf-4da4-ad2c-36117b074c57/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /DphHOM \ --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/stgf8f4bade-64cf-4da4-ad2c-36117b074c57/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:19:11: 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 [2022-11-11T10:16:01+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T10:16:50+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 [2022-11-11T10:16:50+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-hb-03.spider.surfsara.nl <========= [2022-11-11T10:16:50+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-j7fh8axw v11 with ID kind-CWLJob/instance-j7fh8axw to 0 [2022-11-11T10:16:50+0100] [MainThread] [W] [toil.leader] Job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v12 is completely failed [2022-11-11T10:17:15+0100] [MainThread] [I] [toil.leader] Finished toil run with 7 failed jobs. [2022-11-11T10:17:15+0100] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'CWLScatter' kind-CWLScatter/instance-_mc0qzcx v3 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v12 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-g4_gkitb v2 'CWLWorkflow' kind-CWLWorkflow/instance-v82q2za1 v2 'CWLGather' kind-CWLGather/instance-oexto2bs v3 'CWLScatter' kind-CWLScatter/instance-q807kyp6 v2 'CWLWorkflow' kind-CWLWorkflow/instance-jlxu1qh5 v2 [2022-11-11T10:17:15+0100] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpidflinbp) 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/tmpidflinbp' contains 7 failed jobs: 'CWLScatter' kind-CWLScatter/instance-_mc0qzcx v3, 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v12, 'CWLJob' bf_remove_double_tgz.cwl.extract_metadata.extract_metadata.cwl kind-CWLJob/instance-g4_gkitb v2, 'CWLWorkflow' kind-CWLWorkflow/instance-v82q2za1 v2, 'CWLGather' kind-CWLGather/instance-oexto2bs v3, 'CWLScatter' kind-CWLScatter/instance-q807kyp6 v2, 'CWLWorkflow' kind-CWLWorkflow/instance-jlxu1qh5 v2 Log from job "'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v12" follows: =========> [2022-11-11T10:11:33+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-11-11T10:11:33+0100] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host wn-hb-03.spider.surfsara.nl. [2022-11-11T10:11:33+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v10 [2022-11-11T10:11:34+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v10) from description 'CWLJob' bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl kind-CWLJob/instance-j7fh8axw v10 [2022-11-11T10:11:34+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. [2022-11-11T10:11:34+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run/workflows/bf_remove_double_tgz/workflow [2022-11-11T10:11:34+0100] [MainThread] [I] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] /tmp/tmpxh5j6pnb$ singularity \ --quiet \ exec \ --contain \ --ipc \ --cleanenv \ --userns \ --home \ /tmp/tmpxh5j6pnb:/DphHOM \ --bind \ /tmp/tmp7pcnleck:/tmp \ --bind \ /tmp/tmp72qk9_cd/out/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:/var/lib/cwl/stgf8f4bade-64cf-4da4-ad2c-36117b074c57/LOFAR_PULSAR_ARCHIVE_locus030_L229427_red_82518d8e.tar:ro \ --pwd \ /DphHOM \ --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/stgf8f4bade-64cf-4da4-ad2c-36117b074c57/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:19:11: 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 [2022-11-11T10:16:01+0100] [MainThread] [W] [cwltool] [job bf_remove_double_tgz.cwl.eliminate_double_tgz.double_tgz_elimination.cwl] exited with status: 1 [2022-11-11T10:16:50+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 [2022-11-11T10:16:50+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