dnaAlignParts.sh doesn't check for R2 Fastq Pass

[denriquez]

When large fastqs are split because they are too big, there is no check to see if R2 finished splitting properly. It does check to see if the R2 fastq exists, however, during the last stage of splitting which gzips it, the fastq will exist but will still be in the process of being zipped up.

[PedalheadPHX]

Why are we splitting FASTQ, what is the situation when this occurs? If this is really needed we should be doing at the BCL conversion step @denriquez @tgenahmet @awchrist @ryanrichholt

[denriquez]

We actually talked about this in person before but I don't think you remember. Splitting FASTQ doesn't happen for every FASTQ. This happens when the FASTQ is larger than 36 GB. Also, the project that is going through this step wasn't sequenced here.

[PedalheadPHX]

Is it genomes?

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Jonathan Keats Director of Bioinformatics & Assistant Professor Translational Genomics Research Institute

445 North Fifth Street, Phoenix, AZ, 85004 p: 602-343-8690 c: 480-543-0634 jkeats@tgen.org | www.keatslab.org | www.tgen.org

On Jul 27, 2017, at 14:32, denriquez notifications@github.com wrote:

We actually talked about this in person before but I don't think you remember. Splitting FASTQ doesn't happen for every FASTQ. This happens when the FASTQ is larger than 36 GB. Also, the project that is going through this step wasn't sequenced here.

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[denriquez]

Yes

[PedalheadPHX]

Can you add a card to the pipeline development trello board about speed optimization and if one task will be testing FASTQ splitting versus not and if split if we should be interweaving the reads

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Jonathan Keats Director of Bioinformatics & Assistant Professor Translational Genomics Research Institute

445 North Fifth Street, Phoenix, AZ, 85004 p: 602-343-8690 c: 480-543-0634 jkeats@tgen.org | www.keatslab.org | www.tgen.org

On Jul 28, 2017, at 14:56, denriquez notifications@github.com wrote:

Yes

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