Issue #9 new
JC Grenier
created an issue

Hi Nicola, thanks for that new release! I'm hoping to get a lot from it!
I'm trying to run it on some of my samples and have some troubles with it.

Here's what I've launched :

gunzip -c input/Sample_AAR.fastq.gz | ./metaphlan2.py --input_type multifastq --mpa_pkl db_v20/mpa_v20_m200.pkl --bowtie2db db_v20/mpa_v20_m200 --nproc 12 --bowtie2out bam/Sample_AAR.bt2out.txt > profiles/Sample_AAR.mpa.txt

Where my fastq.gz file contains concatenated fastq paired-end files.

Here's the error that I'm getting :

Warning! Biom python library not detected! Exporting to biom format will not work!
IOError: fatal error running BowTie2.
Error while flushing and closing output
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-align --wrapper basic-0 --quiet --sam-no-hd --sam-no-sq --very-sensitive -x db_v20/mpa_v20_m200 -p 12 --passthrough -U -

What do you think it is?

Thanks a lot.

Comments (1)

  1. Nicola Segata repo owner

    Hi,
    we usually see errors like that when, for some reasons, the BowTie2 output file cannot be written. This can happen because the disk is full or because the location is not accessible. For example, does the "bam/" folder (where you want the bowtie2 output to be stored) exist?

    The warning about not having Biom installed is not affecting your run, because you are not specifying "--biom".

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