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Error when performing "make test"

Open euduca opened this issue 7 years ago • 0 comments

Hello. I got this error. Link to testLog.txt: click

$ make test [...] ./nanopore/pipeline.sh tests testJobTree testLog.txt 4 singleMachine 8589934592 make: *** [test] Error 1

Got message from job at time: 1509127924.78 : Hmm with highest likelihood: -2431613448.59
Got message from job at time: 1509127931.15 : Starting analysis Hmm for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis GlobalCoverage for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis LocalCoverage for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis Substitutions for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis Indels for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis AlignmentUncertainty for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis ChannelMappability for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis KmerAnalysis for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis IndelKmerAnalysis for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Only failed jobs and their dependents (4 total) are remaining, so exiting.
Finished the main loop
Waiting for stats collator process to finish
Stats finished collating in 0.479724168777 seconds
Traceback (most recent call last):
  File "./nanopore/pipeline.py", line 214, in <module>
    main()
  File "/ibers/ernie/home/eac16/local/nanopore/nanopore/pipeline.py", line 210, in main
    raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs

Can you help me?

My best regards.

euduca avatar Oct 27 '17 18:10 euduca