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cfe-lab / mixed-hcv

Detected mixed genotype HCV infections by mapping short read data to reference genomes
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Mixed HCV tanking #5

Closed greenbeard1 closed 8 years ago

greenbeard1 commented 9 years ago

Something upstream of Bowtie seems to failing in mixed hcv.

Standard error

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Traceback (most recent call last):
  File "/data/kive/Sandboxes/userart_run138_1L_FB9/step1/random-primer-hcv.py", line 54, in <module>
    main()
  File "/data/kive/Sandboxes/userart_run138_1L_FB9/step1/random-primer-hcv.py", line 49, in main
    n_threads=BOWTIE_THREADS
  File "/data/kive/Sandboxes/userart_run138_1L_FB9/step1/helper.py", line 252, in mixed_hcv
    min_match_len=min_match_len, min_mapq=min_mapq, min_score=min_score, cache=cache
  File "/data/kive/Sandboxes/userart_run138_1L_FB9/step1/helper.py", line 153, in do_map
    if cache_file is not None:
NameError: global name 'cache_file' is not defined
Error while flushing and closing output
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT)
rhliang commented 9 years ago

Note: this was using an outdated version of the pipeline (v1.0-1; at the time of running, v1.0-2 was the newest). v1.0-2 fixes this issue, but still crashes because the output file did not conform to the expected CompoundDatatype. I made a new version (v1.0-3) that relaxes the CompoundDatatype; when Jeff gets a chance we'll run it and see if it works now.

donkirkby commented 8 years ago

Can we close this issue, @greenbeard1?

greenbeard1 commented 8 years ago

Hi, Yes we can close this issue. Cheers and thanks! J

On Wed, Jun 15, 2016 at 1:57 PM, Don Kirkby notifications@github.com wrote:

Can we close this issue, @greenbeard1 https://github.com/greenbeard1?

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