Open bounlu opened 2 years ago
I came up with this issue:
W/w/jobVzpHM5 INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- W/w/jobVzpHM5 INFO:toil:Running Toil version 3.15.0a1-13ed4407b96b3f18717e95501812da4dccb254a1. W/w/jobVzpHM5 [job demux_se.cwl] /eCLIP-Seq/outDir/out_tmpdircWGsfJ$ umi_tools \ W/w/jobVzpHM5 extract \ W/w/jobVzpHM5 --random-seed \ W/w/jobVzpHM5 1 \ W/w/jobVzpHM5 --stdin \ W/w/jobVzpHM5 /eCLIP-Seq/outDir/tmppYFFJR/stg0d62623c-c6e1-4a8c-a437-3912683358cd/SRR14322285.trimmed.fastq.gz \ W/w/jobVzpHM5 --bc-pattern \ W/w/jobVzpHM5 NNNNNNNNNN \ W/w/jobVzpHM5 --log \ W/w/jobVzpHM5 NOVA1.SRR14322285.trimmed.---.--.metrics \ W/w/jobVzpHM5 NOVA1 \ W/w/jobVzpHM5 --stdout \ W/w/jobVzpHM5 NOVA1.SRR14322285.trimmed.umi.r1.fq W/w/jobVzpHM5 INFO:cwltool:[job demux_se.cwl] /eCLIP-Seq/outDir/out_tmpdircWGsfJ$ umi_tools \ W/w/jobVzpHM5 extract \ W/w/jobVzpHM5 --random-seed \ W/w/jobVzpHM5 1 \ W/w/jobVzpHM5 --stdin \ W/w/jobVzpHM5 /eCLIP-Seq/outDir/tmppYFFJR/stg0d62623c-c6e1-4a8c-a437-3912683358cd/SRR14322285.trimmed.fastq.gz \ W/w/jobVzpHM5 --bc-pattern \ W/w/jobVzpHM5 NNNNNNNNNN \ W/w/jobVzpHM5 --log \ W/w/jobVzpHM5 NOVA1.SRR14322285.trimmed.---.--.metrics \ W/w/jobVzpHM5 NOVA1 \ W/w/jobVzpHM5 --stdout \ W/w/jobVzpHM5 NOVA1.SRR14322285.trimmed.umi.r1.fq W/w/jobVzpHM5 Traceback (most recent call last): W/w/jobVzpHM5 File "/opt/conda/bin/umi_tools", line 11, in <module> W/w/jobVzpHM5 sys.exit(main()) W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/umi_tools/umi_tools.py", line 58, in main W/w/jobVzpHM5 module = importlib.import_module("umi_tools." + command, "umi_tools") W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/importlib/__init__.py", line 37, in import_module W/w/jobVzpHM5 __import__(name) W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/umi_tools/extract.py", line 158, in <module> W/w/jobVzpHM5 import umi_tools.extract_methods as extract_methods W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/umi_tools/extract_methods.py", line 7, in <module> W/w/jobVzpHM5 import umi_tools.Utilities as U W/w/jobVzpHM5 ImportError: No module named Utilities W/w/jobVzpHM5 [job demux_se.cwl] Job error: W/w/jobVzpHM5 Error collecting output for parameter 'demuxedAfwd': W/w/jobVzpHM5 :1:1: Did not find output file with glob pattern: '['NOVA1.SRR14322285.trimmed.umi.r1.fq']' W/w/jobVzpHM5 ERROR:cwltool:[job demux_se.cwl] Job error: W/w/jobVzpHM5 Error collecting output for parameter 'demuxedAfwd': W/w/jobVzpHM5 :1:1: Did not find output file with glob pattern: '['NOVA1.SRR14322285.trimmed.umi.r1.fq']' W/w/jobVzpHM5 [job demux_se.cwl] completed permanentFail W/w/jobVzpHM5 WARNING:cwltool:[job demux_se.cwl] completed permanentFail W/w/jobVzpHM5 Traceback (most recent call last): W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/toil-3.15.0a1-py2.7.egg/toil/worker.py", line 313, in workerScript W/w/jobVzpHM5 job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/toil-3.15.0a1-py2.7.egg/toil/job.py", line 1327, in _runner W/w/jobVzpHM5 returnValues = self._run(jobGraph, fileStore) W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/toil-3.15.0a1-py2.7.egg/toil/job.py", line 1272, in _run W/w/jobVzpHM5 return self.run(fileStore) W/w/jobVzpHM5 File "/opt/conda/lib/python2.7/site-packages/toil-3.15.0a1-py2.7.egg/toil/cwl/cwltoil.py", line 461, in run W/w/jobVzpHM5 raise cwltool.errors.WorkflowException(status) W/w/jobVzpHM5 WorkflowException: permanentFail W/w/jobVzpHM5 ERROR:toil.worker:Exiting the worker because of a failed job on host xxx W/w/jobVzpHM5 WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///opt/eclip-0.3.99/cwl/demux_se.cwl' umi_tools extract W/w/jobVzpHM5 with ID W/w/jobVzpHM5 to 1
That's right, umi_tools should be installed using Python3
I came up with this issue: