Attempting to run marginCall on a .sam produced by minimap2. Built according to readme (using a venv) and all tests passed.
Getting the below error, any ideas?
The job seems to have left a log file, indicating failure: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job
Reporting file: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run
log.txt: func(*((self,) + tuple(self.args)), self.kwargs)
log.txt: File "/home/ng384/software/builds/marginAlign/src/margin/utils.py", line 171, in paralleliseSamProcessingTargetFn
log.txt: tempExonerateFileHandle.write(getExonerateCigarFormatString(aR, sam) + "\n")
log.txt: File "/home/ng384/software/builds/marginAlign/src/margin/utils.py", line 50, in getExonerateCigarFormatString
log.txt: assert sum([ op.length for op in pA.operationList if op.type == \
log.txt: AttributeError: 'NoneType' object has no attribute 'operationList'**
log.txt: Exiting the slave because of a failed job on host login-l-1
log.txt: Due to failure we are reducing the remaining retry count of job /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648 bytes
Job: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job is completely failed
Traceback (most recent call last):
File "/home/ng384/software/builds/marginAlign/src/margin/marginCaller.py", line 63, in
main()
File "/home/ng384/software/builds/marginAlign/src/margin/marginCaller.py", line 59, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs
Hi there,
Attempting to run marginCall on a .sam produced by minimap2. Built according to readme (using a venv) and all tests passed.
Getting the below error, any ideas?
The job seems to have left a log file, indicating failure: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job Reporting file: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/ng384/software/builds/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run log.txt: func(*((self,) + tuple(self.args)), self.kwargs) log.txt: File "/home/ng384/software/builds/marginAlign/src/margin/utils.py", line 171, in paralleliseSamProcessingTargetFn log.txt: tempExonerateFileHandle.write(getExonerateCigarFormatString(aR, sam) + "\n") log.txt: File "/home/ng384/software/builds/marginAlign/src/margin/utils.py", line 50, in getExonerateCigarFormatString log.txt: assert sum([ op.length for op in pA.operationList if op.type == \ log.txt: AttributeError: 'NoneType' object has no attribute 'operationList'** log.txt: Exiting the slave because of a failed job on host login-l-1 log.txt: Due to failure we are reducing the remaining retry count of job /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /rds/project/who1000/rds-who1000-wgs10k/WGS10K/data/projects/nanopore/us/analysis/PromethION_temp/NND/G008984/variant_calling/marginCaller/jobTree/jobs/job is completely failed Traceback (most recent call last): File "/home/ng384/software/builds/marginAlign/src/margin/marginCaller.py", line 63, in
main()
File "/home/ng384/software/builds/marginAlign/src/margin/marginCaller.py", line 59, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs