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heathsc / gemBS-rs

A re-write of the gemBS pipeline framework in Rust
BSD 3-Clause "New" or "Revised" License
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Mapping as non-stranded not recognized in gem-mapper #2

Closed cbreenmachine closed 3 years ago

cbreenmachine commented 3 years ago

Hi Simon,

I am trying to use the gemBS pipeline to process some whole human genome bisulfite sequence data that is single-ended. Specifically, I am trying to run the mapping command with non-stranded reads. The command I am using is gemBS map --read-non-stranded. However, it is unable to run and produces the following information within a few seconds. For what it's worth, I can run gemBS run on the demo dataset provided in the documentation for gemBS version 3 here.

Logfile

The logfile gives the following information: (base) bash-4.2$ cat single_map_sample001_101.log /ua/cebreen/lib/gemBS/bin/gem-mapper: unrecognized option '--bisulfite-conversion non-stranded' GEM-Mapper error: Option not recognized samtools sort: failed to read header from "-"`

Condensed terminal output (when running in debug mode)

INFO - Launch: /ua/cebreen/lib/gemBS/bin/gem-mapper --threads 4 -I ./../index/GRCh38.primary_assembly.BS.gem -i ./fastq_trimmed/sample001_101/sample001_101_L001_R1_trimmed.fq --bisulfite-conversion non-stranded --report-file ./mapping/sample001_101.json --sam-read-group-header @RG\tID:sample001_101\tSM:\tBC:sample001_101\tPU:sample001_101 | /ua/cebreen/lib/gemBS/bin/read_filter ./../index/GRCh38.primary_assembly.gemBS.contig_md5 | /ua/cebreen/lib/gemBS/bin/samtools sort -o ./mapping/sample001_101.bam -T ./mapping --threads 4 --write-index - DEBUG - Try to remove output file ./mapping/sample001_101.bam DEBUG - Try to remove output file ./mapping/sample001_101.json DEBUG - Try to remove output file ./mapping/sample001_101.bam.csi DEBUG - Worker thread 7 shutting down after error Error from pipeline: /ua/cebreen/lib/gemBS/bin/samtools exited with error ERROR - Error received from worker thread 7 DEBUG - Job loop finished - cleaning up ERROR - Worker thread 4 received error: receiving on a closed channel ERROR - Worker thread 2 received error: receiving on a closed channel DEBUG - Worker thread 2 shutting down DEBUG - Worker thread 4 shutting down ERROR - Worker thread 5 received error: receiving on a closed channel DEBUG - Worker thread 5 shutting down ERROR - Worker thread 1 received error: receiving on a closed channel DEBUG - Worker thread 1 shutting down ERROR - Worker thread 3 received error: receiving on a closed channel DEBUG - Worker thread 3 shutting down ERROR - Worker thread 6 received error: receiving on a closed channel DEBUG - Worker thread 6 shutting down ERROR - Worker thread 0 received error: receiving on a closed channel DEBUG - Worker thread 0 shutting down Error: "Exiting after error"

Is there anything glaringly obvious I'm messing up? I will continue to try to find the source of the error or at least more information! Please let me know if I can provide anything specific that would help. Thanks in advance!

Best, Coleman

heathsc commented 3 years ago

Thank you for the report - this was a previously unreported bug that I have now fixed and pushed to the repo (just a typo). I will remake the Singularity and docker containers, but this will take a few hours.

Cheers, Simon

cbreenmachine commented 3 years ago

Thanks so much Simon! That's great!

Best, Coleman