error in rule bigwig

[rrdavis77]

When running ARMOR on some data I get an error when it is trying to generate the bigwig files.
Error in rule bigwig: jobid: 51 output: Jin/output/STARbigwig/p63KO35_Aligned.sortedByCoord.out.bw log: Jin/output/logs/bigwig_p63KO35.log (check log file(s) for error message) conda-env: /home/ryan/ARMOR/.snakemake/conda/74957150 shell: echo 'bedtools version: ' > Jin/output/logs/bigwig_p63KO35.log; bedtools --version >> Jin/output/logs/bigwig_p63KO35.log; bedtools genomecov -split -ibam Jin/output/STAR/p63KO35/p63KO35_Aligned.sortedByCoord.out.bam -bg | sort -k1,1 -k2,2n > Jin/output/STARbigwig/p63KO35_Aligned.sortedByCoord.out.bedGraph; bedGraphToBigWig Jin/output/STARbigwig/p63KO35_Aligned.sortedByCoord.out.bedGraph /home/ryan/ARMOR/reference/human/STARIndex/Homo_sapiens.GRCh38.V30.STAR.idx/chrNameLength.txt Jin/output/STARbigwig/p63KO35_Aligned.sortedByCoord.out.bw; rm -f Jin/output/STARbigwig/p63KO35_Aligned.sortedByCoord.out.bedGraph

In the terminal i see:
Jin/output/STARbigwig/p63KO35_Aligned.sortedByCoord.out.bedGraph is not case-sensitive sorted at line 38881834. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.

when looking at that specific line, we see:

`sed -n '38881833,38881835p' p63KO35_Aligned.sortedByCoord.out.bedGraph

chrY 57215886 57215994 1

GL000008.2 83526 83545 1

GL000008.2 85565 85566 1
`
I am using the Genome sequence, primary assembly (GRCh38) from gencode.

Not sure how to proceed. Thanks!

[csoneson]

Not at a stable connection right now, but we do have sort -k1,1 -k2,2n in the bigwig rule, so it may be a problem with the LC_COLLATE=C part. Could you try to see whether adding LC_COLLATE=C just before sort here helps:

ARMOR/Snakefile

Line 471 in 3bfc403

"bedtools genomecov -split -ibam {input.bam} -bg | sort -k1,1 -k2,2n > "

[rrdavis77]

I'll add it and let you know if that solves it.
Thanks

[rrdavis77]

I changed the snake file line 471 by adding LC_COLLATE=C and it solved the issue.

"bedtools genomecov -split -ibam {input.bam} -bg | LC_COLLATE=C sort -k1,1 -k2,2n > "

[csoneson]

Great, thanks. We’ll fix that.