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karel-brinda / rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
http://karel-brinda.github.io/rnftools
MIT License
14 stars 5 forks source link

Devel linux build fails on Travis #66

Open simonepignotti opened 6 years ago

simonepignotti commented 6 years ago

The build for the devel branch fails with an error which seems not to be related to the changes in such branch: https://travis-ci.org/karel-brinda/rnftools/jobs/397415103

=======================================================
/home/travis/build/karel-brinda/rnftools/examples/01_tutorial/03_evaluation/03_evaluation
=======================================================

...

Finished job 9.
10 of 16 steps (62%) done
rule 5:
    input: report_SE/0/gp/_combined.gp, report_SE/0/roc/bwa-mem.roc, report_SE/0/roc/bwa-sw.roc
    output: report_SE/0/graphics/_combined_0.svg, report_SE/0/graphics/_combined_1.svg, report_SE/0/graphics/_combined_2.svg, report_SE/0/graphics/_combined_3.svg, report_SE/0/graphics/_combined_4.svg, report_SE/0/graphics/_combined_0.pdf, report_SE/0/graphics/_combined_1.pdf, report_SE/0/graphics/_combined_2.pdf, report_SE/0/graphics/_combined_3.pdf, report_SE/0/graphics/_combined_4.pdf, report_SE/0/tar/report_SE.dir 0.tar
    jobid: 2
Building DAG of jobs...
Using shell: /bin/bash
Job counts:
    count   jobs
    1   5
    1
'report_SE/0/graphics/_combined_0.pdf' was created from 'report_SE/0/graphics/_combined_0.svg' using function 'svg42pdf_cairo'.
'report_SE/0/graphics/_combined_1.pdf' was created from 'report_SE/0/graphics/_combined_1.svg' using function 'svg42pdf_cairo'.
'report_SE/0/graphics/_combined_2.pdf' was created from 'report_SE/0/graphics/_combined_2.svg' using function 'svg42pdf_cairo'.
'report_SE/0/graphics/_combined_3.pdf' was created from 'report_SE/0/graphics/_combined_3.svg' using function 'svg42pdf_cairo'.
'report_SE/0/graphics/_combined_4.pdf' was created from 'report_SE/0/graphics/_combined_4.svg' using function 'svg42pdf_cairo'.
    Error in rule 5:
        jobid: 0
        output: report_SE/0/graphics/_combined_0.svg, report_SE/0/graphics/_combined_1.svg, report_SE/0/graphics/_combined_2.svg, report_SE/0/graphics/_combined_3.svg, report_SE/0/graphics/_combined_4.svg, report_SE/0/graphics/_combined_0.pdf, report_SE/0/graphics/_combined_1.pdf, report_SE/0/graphics/_combined_2.pdf, report_SE/0/graphics/_combined_3.pdf, report_SE/0/graphics/_combined_4.pdf, report_SE/0/tar/report_SE.dir 0.tar
RuleException:
FileNotFoundError in line 52 of /home/travis/miniconda/envs/rnftools/lib/python3.6/site-packages/rnftools/lavender/lavender.snake:
[Errno 2] No such file or directory: 'report_SE/0/gp/bwa-mem.gp'
  File "/home/travis/miniconda/envs/rnftools/lib/python3.6/site-packages/rnftools/lavender/lavender.snake", line 52, in __rule_9
  File "/home/travis/miniconda/envs/rnftools/lib/python3.6/site-packages/rnftools/lavender/Panel.py", line 371, in create_tar
  File "/home/travis/miniconda/envs/rnftools/lib/python3.6/site-packages/rnftools/lavender/Panel.py", line 334, in add_file_to_tar
  File "/home/travis/miniconda/envs/rnftools/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Removing output files of failed job 5 since they might be corrupted:
report_SE/0/graphics/_combined_0.svg, report_SE/0/graphics/_combined_1.svg, report_SE/0/graphics/_combined_2.svg, report_SE/0/graphics/_combined_3.svg, report_SE/0/graphics/_combined_4.svg, report_SE/0/graphics/_combined_0.pdf, report_SE/0/graphics/_combined_1.pdf, report_SE/0/graphics/_combined_2.pdf, report_SE/0/graphics/_combined_3.pdf, report_SE/0/graphics/_combined_4.pdf, report_SE/0/tar/report_SE.dir 0.tar
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/travis/build/karel-brinda/rnftools/examples/01_tutorial/03_evaluation/03_evaluation/.snakemake/log/2018-06-27T161917.543517.snakemake.log
make[3]: *** [all] Error 1
make[3]: Leaving directory `/home/travis/build/karel-brinda/rnftools/examples/01_tutorial/03_evaluation/03_evaluation'
make[2]: *** [03_evaluation/] Error 2
make[2]: Leaving directory `/home/travis/build/karel-brinda/rnftools/examples/01_tutorial/03_evaluation'
make[1]: *** [03_evaluation/] Error 2
make[1]: Leaving directory `/home/travis/build/karel-brinda/rnftools/examples/01_tutorial'
make: *** [01_tutorial/] Error 2
make: Leaving directory `/home/travis/build/karel-brinda/rnftools/examples'
The command "make -C examples" exited with 2.
Done. Your build exited with 1.

The build for OSX works, and no change was made to the lavender submodule.