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ISUgenomics / SequelTools

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quality control 'the BAM file is empty or does not exist' #6

Closed droeatumn closed 4 years ago

droeatumn commented 4 years ago

Kir5_P1_8_999F_all.contigs_KP420442_sorted.bam.gz subreads.txt I am running today's version on OSX 10.15.4 with the attached files (I gzipped the bam for the sake of uploading). This is what happened:

~/git/SequelTools/Scripts/SequelTools.sh -t Q -u subFiles.txt 
Beginning quality control function

Running in NO_SCRAPS mode
the BAM file  is empty or does not exist
DavidEHufnagel commented 4 years ago

Hello Dave,

Thanks for trying out our program! The issue seems to be that you set the file of BAM input files to "subFiles.txt" rather than to your file, "subreads.txt". Give that a shot and let me know if it doesn't work out!

Best, David E. Hufnagel

On Fri, Apr 3, 2020 at 7:22 PM Dave Roe notifications@github.com wrote:

Kir5_P1_8_999F_all.contigs_KP420442_sorted.bam.gz https://github.com/ISUgenomics/SequelTools/files/4430459/Kir5_P1_8_999F_all.contigs_KP420442_sorted.bam.gz subreads.txt https://github.com/ISUgenomics/SequelTools/files/4430460/subreads.txt I am running today's version on OSX 10.15.4 with the attached files (I gzipped the bam for the sake of uploading). This is what happened:

~/git/SequelTools/Scripts/SequelTools.sh -t Q -u subFiles.txt Beginning quality control function

Running in NO_SCRAPS mode the BAM file is empty or does not exist

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droeatumn commented 4 years ago

You are correct. Thank you!

DavidEHufnagel commented 4 years ago

no worries!

On Tue, Apr 7, 2020 at 10:42 AM Dave Roe notifications@github.com wrote:

You are correct. Thank you!

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