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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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RNA-Seq pipeline stopping after trim galore #95

Closed kerimsecener closed 3 years ago

kerimsecener commented 3 years ago

Hello,

I'm running pigx-rnaseq on three samples (paired-end): trim_galore log files seem fine to me, however in the snakejob log files I see this:

_mv: cannot stat ‘/fast/CF_Sequencing/work_dir/cfische/SP005/bulk_RNA_seq/pigx_work/pigx_output/trimmed_reads/GYWU-1219_EIA5_CTNNB1R1.good.fq.gz’: No such file or directory

"_GYWU-1219_EIA5_CTNNB1R1.good.fq.gz " is supposed to be the original fastq file name, I don't understand why the algorithm looks for it in the trimmed_reads folder ?

I'm attaching the yaml file, sample sheet, as well as error files. settings.yaml.txt trim_galore_GYWU_1219.log snakejob.trim_galore_pe.7.sh.e4460475.txt sample_sheet.csv

Thanks,

Kerim

borauyar commented 3 years ago

Hi Kerim, I made a new release replacing trim galore with a faster/better alternative. https://github.com/BIMSBbioinfo/pigx_rnaseq/releases/tag/v0.0.13

The guix package for this release should be available within a couple of days. Best, Bora