Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error when performing "make test" #10

Open
euduca opened this issue Oct 27, 2017 · 0 comments
Open

Error when performing "make test" #10

euduca opened this issue Oct 27, 2017 · 0 comments
Assignees

Comments

@euduca
Copy link

euduca commented Oct 27, 2017

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.

@mitenjain mitenjain self-assigned this Oct 27, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants