After successfully installing Cactus and The comparative genomics toolkit, I get a multiple set of errors when running Hal2Assembly with --cladeExclusiveRegions command.
2022-10-20T09:38:31-0400] [MainThread] [I] [toil.job] Saving graph of 1 jobs, 1 new [2022-10-20T09:38:31-0400] [MainThread] [I] [toil.job] Processing job 'Setup' kind-Setup/instance-napj81cd v0 [2022-10-20T09:38:31-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:38:32-0400] [MainThread] [I] [toil.leader] Issued job 'Setup' kind-Setup/instance-napj81cd v1 with job batch system ID: 0 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:32-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/81ac/worker_log.txt [2022-10-20T09:38:34-0400] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-_35rnqio v1 with job batch system ID: 1 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-p0hfi14_ v1 with job batch system ID: 2 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-m2suoz7y v1 with job batch system ID: 3 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-jmew0y80 v1 with job batch system ID: 4 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-kzsb_of_ v1 with job batch system ID: 5 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/0de2/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/b39b/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/934b/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/e0fe/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/b36f/worker_log.txt [2022-10-20T09:39:07-0400] [MainThread] [I] [toil.leader] Issued job 'MakeTracks' kind-MakeTracks/instance-630ocjqm v1 with job batch system ID: 6 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:07-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/4267/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-751dm0mo v1 with job batch system ID: 7 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-xpybyd94 v1 with job batch system ID: 8 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-933zrn7v v1 with job batch system ID: 9 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusiveRegions' kind-GetCladeExclusiveRegions/instance-rb0v4psb v1 with job batch system ID: 10 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'MakeAnnotationTracks' kind-MakeAnnotationTracks/instance-nyei8hka v1 with job batch system ID: 11 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-e1raire7 v1 with job batch system ID: 12 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'MakeAnnotationTracks' kind-MakeAnnotationTracks/instance-_vj78hnf v1 with job batch system ID: 13 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'MakeAnnotationTracks' kind-MakeAnnotationTracks/instance-lq8i08yo v1 with job batch system ID: 14 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-trvb4k42 v1 with job batch system ID: 15 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/4ad5/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/bbbf/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/da97/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/6544/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/6144/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/e016/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/0e6d/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/9b92/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/7743/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 with job batch system ID: 16 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 with job batch system ID: 17 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 with job batch system ID: 18 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 with job batch system ID: 19 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 with job batch system ID: 20 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/9755/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/a7d2/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/041c/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/600b/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/f533/worker_log.txt [2022-10-20T10:17:18-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-6828015s. [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 Exit reason: None [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v2 [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-6828015s" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc0/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bb exited with non-zero status 255 [2022-10-20T10:17:18-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc0', 'Espez', 'Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0 <========= [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v2 with ID kind-GetCladeExclusive/instance-6828015s to 1 [2022-10-20T10:17:18-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v3 with job batch system ID: 21 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/abd7/worker_log.txt [2022-10-20T10:38:34-0400] [MainThread] [I] [toil.leader] 10 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T10:55:50-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-6828015s. [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v3 Exit reason: None [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v5 [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-6828015s" follows: =========> [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T10:17:19-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc0/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bb exited with non-zero status 255 [2022-10-20T10:55:50-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc0', 'Espez', 'Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0 <========= [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v5 with ID kind-GetCladeExclusive/instance-6828015s to 0 [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6 is completely failed [2022-10-20T11:38:35-0400] [MainThread] [I] [toil.leader] 7 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T12:14:27-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-mniubdym. [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 Exit reason: None [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v2 [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-mniubdym" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc1/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bb exited with non-zero status 255 [2022-10-20T12:14:27-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1 <========= [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v2 with ID kind-GetCladeExclusive/instance-mniubdym to 1 [2022-10-20T12:14:27-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v3 with job batch system ID: 22 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/6b59/worker_log.txt [2022-10-20T12:28:00-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-606j2aes. [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 Exit reason: None [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v2 [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-606j2aes" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed is not case-sensitive sorted at line 825553. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Espez/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bb exited with non-zero status 255 [2022-10-20T12:28:00-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Espez'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez <========= [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v2 with ID kind-GetCladeExclusive/instance-606j2aes to 1 [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v3 with job batch system ID: 23 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/76ef/worker_log.txt [2022-10-20T12:38:36-0400] [MainThread] [I] [toil.leader] 7 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T13:38:37-0400] [MainThread] [I] [toil.leader] 5 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T14:03:12-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-mniubdym. [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v3 Exit reason: None [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v5 [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-mniubdym" follows: =========> [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:14:29-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 [2022-10-20T12:14:30-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc1/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bb exited with non-zero status 255 [2022-10-20T14:03:12-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1 <========= [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v5 with ID kind-GetCladeExclusive/instance-mniubdym to 0 [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6 is completely failed [2022-10-20T14:08:23-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-w5osf6h6. [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 Exit reason: None [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v2 [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-w5osf6h6" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed is not case-sensitive sorted at line 2318069. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Htub/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bb exited with non-zero status 255 [2022-10-20T14:08:23-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub <========= [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v2 with ID kind-GetCladeExclusive/instance-w5osf6h6 to 1 [2022-10-20T14:08:23-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v3 with job batch system ID: 24 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/e4bf/worker_log.txt [2022-10-20T14:30:26-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-bltwesc6. [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 Exit reason: None [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v2 [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-bltwesc6" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed is not case-sensitive sorted at line 2213530. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Hery/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bb exited with non-zero status 255 [2022-10-20T14:30:26-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Hery'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery <========= [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v2 with ID kind-GetCladeExclusive/instance-bltwesc6 to 1 [2022-10-20T14:30:26-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v3 with job batch system ID: 25 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/a888/worker_log.txt [2022-10-20T14:38:38-0400] [MainThread] [I] [toil.leader] 3 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T15:15:43-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-606j2aes. [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v3 Exit reason: None [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v5 [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-606j2aes" follows: =========> [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:28:00-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed is not case-sensitive sorted at line 825553. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Espez/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bb exited with non-zero status 255 [2022-10-20T15:15:43-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Espez'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez <========= [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v5 with ID kind-GetCladeExclusive/instance-606j2aes to 0 [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6 is completely failed [2022-10-20T15:38:40-0400] [MainThread] [I] [toil.leader] 2 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T16:38:40-0400] [MainThread] [I] [toil.leader] 2 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T17:29:15-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-w5osf6h6. [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v3 Exit reason: None [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v5 [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-w5osf6h6" follows: =========> [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:08:24-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 [2022-10-20T14:08:25-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed is not case-sensitive sorted at line 2318069. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Htub/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bb exited with non-zero status 255 [2022-10-20T17:29:15-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub <========= [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v5 with ID kind-GetCladeExclusive/instance-w5osf6h6 to 0 [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6 is completely failed [2022-10-20T17:38:41-0400] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T18:18:26-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-bltwesc6. [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v3 Exit reason: None [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v5 [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-bltwesc6" follows: =========> [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:30:27-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed is not case-sensitive sorted at line 2213530. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Hery/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bb exited with non-zero status 255 [2022-10-20T18:18:26-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Hery'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery <========= [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v5 with ID kind-GetCladeExclusive/instance-bltwesc6 to 0 [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6 is completely failed [2022-10-20T18:18:41-0400] [MainThread] [I] [toil.leader] Finished toil run with 8 failed jobs. [2022-10-20T18:18:41-0400] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6 'Setup' kind-Setup/instance-napj81cd v2 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6 'GetCladeExclusiveRegions' kind-GetCladeExclusiveRegions/instance-rb0v4psb v2 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6 'MakeTracks' kind-MakeTracks/instance-630ocjqm v2 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6 Traceback (most recent call last): File "/home/ab620/cactus-bin-v2.2.3/bin/hal2assemblyHub.py", line 451, in <module> main() File "/home/ab620/cactus-bin-v2.2.3/bin/hal2assemblyHub.py", line 448, in main toil.start(Setup(options.halfile, options.outputDirectory, options)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/common.py", line 966, in start return self._runMainLoop(rootJobDescription) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/common.py", line 1386, in _runMainLoop return Leader(config=self.config, File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/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 '/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2' contains 8 failed jobs: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6, 'Setup' kind-Setup/instance-napj81cd v2, 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6, 'GetCladeExclusiveRegions' kind-GetCladeExclusiveRegions/instance-rb0v4psb v2, 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6, 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6, 'MakeTracks' kind-MakeTracks/instance-630ocjqm v2, 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6 Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6" follows: =========> [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:14:29-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 [2022-10-20T12:14:30-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc1/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bb exited with non-zero status 255 [2022-10-20T14:03:12-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1 <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6" follows: =========> [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:08:24-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 [2022-10-20T14:08:25-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed is not case-sensitive sorted at line 2318069. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Htub/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bb exited with non-zero status 255 [2022-10-20T17:29:15-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6" follows: =========> [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:30:27-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed is not case-sensitive sorted at line 2213530. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Hery/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bb exited with non-zero status 255 [2022-10-20T18:18:26-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Hery'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6" follows: =========> [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T10:17:19-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc0/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bb exited with non-zero status 255 [2022-10-20T10:55:50-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc0', 'Espez', 'Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0 <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6" follows: =========> [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:28:00-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed is not case-sensitive sorted at line 825553. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Espez/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bb exited with non-zero status 255 [2022-10-20T15:15:43-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Espez'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez
I would appreciate any tips or feedback to run this
After successfully installing Cactus and The comparative genomics toolkit, I get a multiple set of errors when running Hal2Assembly with --cladeExclusiveRegions command.
2022-10-20T09:38:31-0400] [MainThread] [I] [toil.job] Saving graph of 1 jobs, 1 new [2022-10-20T09:38:31-0400] [MainThread] [I] [toil.job] Processing job 'Setup' kind-Setup/instance-napj81cd v0 [2022-10-20T09:38:31-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:38:32-0400] [MainThread] [I] [toil.leader] Issued job 'Setup' kind-Setup/instance-napj81cd v1 with job batch system ID: 0 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:32-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/81ac/worker_log.txt [2022-10-20T09:38:34-0400] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-_35rnqio v1 with job batch system ID: 1 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-p0hfi14_ v1 with job batch system ID: 2 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-m2suoz7y v1 with job batch system ID: 3 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-jmew0y80 v1 with job batch system ID: 4 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:35-0400] [MainThread] [I] [toil.leader] Issued job 'GetBasicFiles' kind-GetBasicFiles/instance-kzsb_of_ v1 with job batch system ID: 5 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/0de2/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/b39b/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/934b/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/e0fe/worker_log.txt [2022-10-20T09:38:36-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/b36f/worker_log.txt [2022-10-20T09:39:07-0400] [MainThread] [I] [toil.leader] Issued job 'MakeTracks' kind-MakeTracks/instance-630ocjqm v1 with job batch system ID: 6 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:07-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/4267/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-751dm0mo v1 with job batch system ID: 7 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-xpybyd94 v1 with job batch system ID: 8 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-933zrn7v v1 with job batch system ID: 9 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusiveRegions' kind-GetCladeExclusiveRegions/instance-rb0v4psb v1 with job batch system ID: 10 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'MakeAnnotationTracks' kind-MakeAnnotationTracks/instance-nyei8hka v1 with job batch system ID: 11 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-e1raire7 v1 with job batch system ID: 12 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'MakeAnnotationTracks' kind-MakeAnnotationTracks/instance-_vj78hnf v1 with job batch system ID: 13 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'MakeAnnotationTracks' kind-MakeAnnotationTracks/instance-lq8i08yo v1 with job batch system ID: 14 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.leader] Issued job 'GetAlignability' kind-GetAlignability/instance-trvb4k42 v1 with job batch system ID: 15 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/4ad5/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/bbbf/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/da97/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/6544/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/6144/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/e016/worker_log.txt [2022-10-20T09:39:08-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/0e6d/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/9b92/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/7743/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 with job batch system ID: 16 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 with job batch system ID: 17 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 with job batch system ID: 18 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 with job batch system ID: 19 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 with job batch system ID: 20 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/9755/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/a7d2/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/041c/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/600b/worker_log.txt [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/f533/worker_log.txt [2022-10-20T10:17:18-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-6828015s. [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 Exit reason: None [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v2 [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-6828015s" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc0/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bb exited with non-zero status 255 [2022-10-20T10:17:18-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc0', 'Espez', 'Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0 <========= [2022-10-20T10:17:18-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v2 with ID kind-GetCladeExclusive/instance-6828015s to 1 [2022-10-20T10:17:18-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v3 with job batch system ID: 21 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/abd7/worker_log.txt [2022-10-20T10:38:34-0400] [MainThread] [I] [toil.leader] 10 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T10:55:50-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-6828015s. [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v3 Exit reason: None [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v5 [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-6828015s" follows: =========> [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T10:17:19-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc0/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bb exited with non-zero status 255 [2022-10-20T10:55:50-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc0', 'Espez', 'Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0 <========= [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v5 with ID kind-GetCladeExclusive/instance-6828015s to 0 [2022-10-20T10:55:50-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6 is completely failed [2022-10-20T11:38:35-0400] [MainThread] [I] [toil.leader] 7 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T12:14:27-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-mniubdym. [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 Exit reason: None [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v2 [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-mniubdym" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc1/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bb exited with non-zero status 255 [2022-10-20T12:14:27-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1 <========= [2022-10-20T12:14:27-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v2 with ID kind-GetCladeExclusive/instance-mniubdym to 1 [2022-10-20T12:14:27-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v3 with job batch system ID: 22 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/6b59/worker_log.txt [2022-10-20T12:28:00-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-606j2aes. [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 Exit reason: None [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v2 [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-606j2aes" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed is not case-sensitive sorted at line 825553. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Espez/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bb exited with non-zero status 255 [2022-10-20T12:28:00-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Espez'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez <========= [2022-10-20T12:28:00-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v2 with ID kind-GetCladeExclusive/instance-606j2aes to 1 [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v3 with job batch system ID: 23 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/76ef/worker_log.txt [2022-10-20T12:38:36-0400] [MainThread] [I] [toil.leader] 7 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T13:38:37-0400] [MainThread] [I] [toil.leader] 5 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T14:03:12-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-mniubdym. [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v3 Exit reason: None [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v5 [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-mniubdym" follows: =========> [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:14:29-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 [2022-10-20T12:14:30-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc1/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bb exited with non-zero status 255 [2022-10-20T14:03:12-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1 <========= [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v5 with ID kind-GetCladeExclusive/instance-mniubdym to 0 [2022-10-20T14:03:12-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6 is completely failed [2022-10-20T14:08:23-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-w5osf6h6. [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 Exit reason: None [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v2 [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-w5osf6h6" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed is not case-sensitive sorted at line 2318069. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Htub/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bb exited with non-zero status 255 [2022-10-20T14:08:23-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub <========= [2022-10-20T14:08:23-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v2 with ID kind-GetCladeExclusive/instance-w5osf6h6 to 1 [2022-10-20T14:08:23-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v3 with job batch system ID: 24 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/e4bf/worker_log.txt [2022-10-20T14:30:26-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-bltwesc6. [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 Exit reason: None [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v2 [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-bltwesc6" follows: =========> [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T09:39:09-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 [2022-10-20T09:39:09-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v1 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed is not case-sensitive sorted at line 2213530. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Hery/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bb exited with non-zero status 255 [2022-10-20T14:30:26-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Hery'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery <========= [2022-10-20T14:30:26-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v2 with ID kind-GetCladeExclusive/instance-bltwesc6 to 1 [2022-10-20T14:30:26-0400] [MainThread] [I] [toil.leader] Issued job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v3 with job batch system ID: 25 and cores: 1, disk: 2.0 Gi, and memory: 2.0 Gi [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Redirecting logging to /tmp/f530ca0d2e025ee7b563db8845d5d3a7/a888/worker_log.txt [2022-10-20T14:38:38-0400] [MainThread] [I] [toil.leader] 3 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T15:15:43-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-606j2aes. [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v3 Exit reason: None [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v5 [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-606j2aes" follows: =========> [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:28:00-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed is not case-sensitive sorted at line 825553. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Espez/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bb exited with non-zero status 255 [2022-10-20T15:15:43-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Espez'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez <========= [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v5 with ID kind-GetCladeExclusive/instance-606j2aes to 0 [2022-10-20T15:15:43-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6 is completely failed [2022-10-20T15:38:40-0400] [MainThread] [I] [toil.leader] 2 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T16:38:40-0400] [MainThread] [I] [toil.leader] 2 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T17:29:15-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-w5osf6h6. [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v3 Exit reason: None [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v5 [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-w5osf6h6" follows: =========> [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:08:24-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 [2022-10-20T14:08:25-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed is not case-sensitive sorted at line 2318069. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Htub/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bb exited with non-zero status 255 [2022-10-20T17:29:15-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub <========= [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v5 with ID kind-GetCladeExclusive/instance-w5osf6h6 to 0 [2022-10-20T17:29:15-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6 is completely failed [2022-10-20T17:38:41-0400] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2022-10-20T18:18:26-0400] [Thread-1 ] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker GetCladeExclusive file:/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2 kind-GetCladeExclusive/instance-bltwesc6. [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v3 Exit reason: None [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v5 [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] Log from job "kind-GetCladeExclusive/instance-bltwesc6" follows: =========> [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:30:27-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed is not case-sensitive sorted at line 2213530. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Hery/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bb exited with non-zero status 255 [2022-10-20T18:18:26-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Hery'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery <========= [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v5 with ID kind-GetCladeExclusive/instance-bltwesc6 to 0 [2022-10-20T18:18:26-0400] [MainThread] [W] [toil.leader] Job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6 is completely failed [2022-10-20T18:18:41-0400] [MainThread] [I] [toil.leader] Finished toil run with 8 failed jobs. [2022-10-20T18:18:41-0400] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6 'Setup' kind-Setup/instance-napj81cd v2 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6 'GetCladeExclusiveRegions' kind-GetCladeExclusiveRegions/instance-rb0v4psb v2 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6 'MakeTracks' kind-MakeTracks/instance-630ocjqm v2 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6 Traceback (most recent call last): File "/home/ab620/cactus-bin-v2.2.3/bin/hal2assemblyHub.py", line 451, in <module> main() File "/home/ab620/cactus-bin-v2.2.3/bin/hal2assemblyHub.py", line 448, in main toil.start(Setup(options.halfile, options.outputDirectory, options)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/common.py", line 966, in start return self._runMainLoop(rootJobDescription) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/common.py", line 1386, in _runMainLoop return Leader(config=self.config, File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/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 '/gpfs/fs1/data/wraycompute/alejo/newhal/jobStore2' contains 8 failed jobs: 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6, 'Setup' kind-Setup/instance-napj81cd v2, 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6, 'GetCladeExclusiveRegions' kind-GetCladeExclusiveRegions/instance-rb0v4psb v2, 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6, 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6, 'MakeTracks' kind-MakeTracks/instance-630ocjqm v2, 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6 Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v6" follows: =========> [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:14:29-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:14:29-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 [2022-10-20T12:14:30-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-mniubdym v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc1/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1/Anc1.bb exited with non-zero status 255 [2022-10-20T14:03:12-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc1 <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v6" follows: =========> [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:08:24-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:08:24-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 [2022-10-20T14:08:25-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-w5osf6h6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed is not case-sensitive sorted at line 2318069. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Htub/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub/Htub.bb exited with non-zero status 255 [2022-10-20T17:29:15-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Htub <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v6" follows: =========> [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T14:30:27-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 [2022-10-20T14:30:27-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-bltwesc6 v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed is not case-sensitive sorted at line 2213530. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Hery/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery/Hery.bb exited with non-zero status 255 [2022-10-20T18:18:26-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Hery'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Hery <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v6" follows: =========> [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T10:17:19-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 [2022-10-20T10:17:19-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-6828015s v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed is empty Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Anc0/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0/Anc0.bb exited with non-zero status 255 [2022-10-20T10:55:50-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Anc0', 'Espez', 'Anc1', 'Hery', 'Htub'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Anc0 <========= Log from job "'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v6" follows: =========> [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-20T12:28:00-0400] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host x3-03-4.genome.duke.edu. [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Working on job 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 [2022-10-20T12:28:00-0400] [MainThread] [I] [toil.worker] Loaded body Job('GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4) from description 'GetCladeExclusive' kind-GetCladeExclusive/instance-606j2aes v4 /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed is not case-sensitive sorted at line 825553. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Traceback (most recent call last): File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/ab620/cactus-bin-v2.2.3/lib/hal/assemblyHub/groupExclusiveRegions.py", line 67, in run system("bedToBigBed %s %s %s" %(outbed, chrsizefile, outbigbed)) File "/gpfs/fs1/home/ab620/cactus-bin-v2.2.3/cactus_env/lib/python3.8/site-packages/sonLib/bioio.py", line 194, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: bedToBigBed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bed /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/../../Espez/chrom.sizes /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/Espez/Espez.bb exited with non-zero status 255 [2022-10-20T15:15:43-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host x3-03-4.genome.duke.edu ['Espez'] /gpfs/fs1/data/wraycompute/alejo/newhal/Hery_halout2/liftoverbeds/CladeExclusive/EspezI would appreciate any tips or feedback to run this