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umi_tools import fails on single end cwl #29

Open bounlu opened 2 years ago

bounlu commented 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
byee4 commented 2 years ago

That's right, umi_tools should be installed using Python3