biobloomcategorizer: invalid option -- 'a'

[mcmero]

I am trying to run tap2 using a bloom filter like so:

tap2.py sample . --bf ../../biobloomtools-2.3.2/test/reads.bf --fq sample_R1.fastq.gz sample_R2.fastq.gz --k 79 49 --readlen 101 --nprocs 1 --params params.ini

However, I'm getting the following exception:

Original exception:

    Exception #1
      'exceptions.Exception(Failed to run '/bin/bash -c "biobloomcategorizer --fq -i -p ./bbt_2.3.2/sample -a 2 -t 1 -e -f ../../biobloomtools-2.3.2/test/reads.bf sample_R1.fastq.gz sample_R2.fastq.gz"'
    biobloomcategorizer: invalid option -- 'a'
    Usage of paired end mode:
    BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [FILEPAIR1] [FILEPAIR2]
    or BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [SMARTPAIR]

    Non-zero exit status 1)' raised in ...
       Task = def classify(...):
       Job  = [[[sample_R1.fastq.gz], [sample_R2.fastq.gz]] -> bbt_2.3.2/sample_reads.fq, bbt_2.3.2/sample, .../test/reads.bf, 1]

    Traceback (most recent call last):
      File "/group/bioi1/marekc/apps/conda2/lib/python2.7/site-packages/ruffus/task.py", line 712, in run_pooled_job_without_exceptions
        register_cleanup, touch_files_only)
      File "/group/bioi1/marekc/apps/conda2/lib/python2.7/site-packages/ruffus/task.py", line 544, in job_wrapper_io_files
        ret_val = user_defined_work_func(*params)
      File "/home/marek.cmero/.local/lib/python2.7/site-packages/pavfinder-1.4.0-py2.7.egg/EGG-INFO/scripts/tap2.py", line 223, in classify
        run_cmd('/bin/bash -c "%s"' % cmd)
      File "/home/marek.cmero/.local/lib/python2.7/site-packages/pavfinder-1.4.0-py2.7.egg/EGG-INFO/scripts/tap2.py", line 31, in run_cmd
        (cmd, stdout_str, stderr_str, process.returncode))
    Exception: Failed to run '/bin/bash -c "biobloomcategorizer --fq -i -p ./bbt_2.3.2/sample -a 2 -t 1 -e -f ../../biobloomtools-2.3.2/test/reads.bf sample_R1.fastq.gz sample_R2.fastq.gz"'
    biobloomcategorizer: invalid option -- 'a'
    Usage of paired end mode:
    BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [FILEPAIR1] [FILEPAIR2]
    or BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [SMARTPAIR]

    Non-zero exit status 1

Looking into biobloomcategorizer, the latest version does not appear to have the -a option. Which version(s) of biobloomcategorizer are compatible with tap?

[sjackman]

cc @JustinChu

[JustinChu]

I think this is version mismatch issue. The -a option was removed a few versions back and moved to biobloommicategorizer

[sjackman]

@readmanchiu Can pavfinder be updated to use the most recent version of BioBloomTools?

@JustinChu If it's possible could the -a option be added back to biobloomcategorizer for compatibility with Pavfinder?

[JustinChu]

It wouldn't be advisable to do so, since all miBF functionality would have to be added back to the executable and it was seperated to avoid confusion between the tools.

[sjackman]

@readmanchiu Sounds like pavfinder should use biobloommicategorizer rather than biobloomcategorizer.

[readmanchiu]

sorry about that, there has been some issues of making the changes to use the latest version of BBT, I will work on that again. The current version of BBT that TAP is compatible with is 2.1.0.

[readmanchiu]

@mcmero I changed tap2 to be compatible with bbt v2.3.3, and now it uses biobloommicategorizer instead of biobloomcategorizer. Just a caveat you may have to adjust the -b parameter when you used biobloommimaker to create your filter (you may have to lower -b if you have fewer than 100 targets). Please consult @JustinChu in this regard. From our end, I'll do more testing to understand the behavior of this new BBT before I tag the release.