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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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samtools empty query name #334

Closed brainfo closed 1 year ago

brainfo commented 1 year ago

Describe the bug I got errors:

[W::sam_parse1] empty query name
[W::sam_read1_sam] Parse error at line 10630
samtools view: error reading file "-"
[W::sam_parse1] empty query name
[W::sam_read1_sam] Parse error at line 12723
samtools view: error reading file "-"

and thus there's no BCstats.txt out.

To Reproduce yaml: prime_seq.yaml.txt

log (which I killed the process while it's running star mapping after the samtools error): primeseq.log

barcode counts from bbduk: stats.txt

fastqc of the two fastqs: These two fastqs were trimmed polyA/polyT (I think some r2 reads get to the polyA region), so the r2 read length may not always get to 150bp. could this be a problem with the cDNA specification in r2 as cDNA(9-150)? AZ_Placenta_PS_2_EKDL220011301-1A_H5HLYDSX5_L1_cutadapt_1_fastqc.zip AZ_Placenta_PS_2_EKDL220011301-1A_H5HLYDSX5_L1_cutadapt_2_fastqc.zip

Desktop (please complete the following information): OS: Ubuntu Version: 20.04.4 LTS zUMIs: version 2.9.7 samtools version: 1.15.1

Best,

cziegenhain commented 1 year ago

the problem is that there are empty reads that were completely trimmed out (0bp).