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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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samtools sort error #34

Closed Deeptirao closed 2 years ago

Deeptirao commented 2 years ago

Please help with this error. I'm using version 2.2.3 installed with conda. In fact, I am providing sorted bams and can skip this step.

qtlseq -r normalised_deepti_sm.fasta -p a93.our_sm.sorted.rmdup.bam -b1 F1.our_sm.sorted.rmdup.bam -b2 F6.our_sm.sorted.rmdup.bam -n1 8 -n2 8 -o qtlseq_output [QTL-seq:2022-06-24 16:37:19] start to run QTL-seq. [QTL-seq:2022-06-24 16:37:19] maximum number of threads which you can use is up to 16. [QTL-seq:2022-06-24 16:37:19] start to index reference fasta. [QTL-seq:2022-06-24 16:42:45] indexing of reference successfully finished. [QTL-seq:2022-06-24 16:42:45] start to merge BAMs. [QTL-seq:2022-06-24 16:42:45] !!ERROR!! samtools sort -m 1G -@ 2 -o qtlseq_output/20_bam/parent.bam qtlseq_output/20_bam/parent.unsorted.bam >> qtlseq_output/log/samtools.log 2>&1

please check below:

open: No such file or directory

YuSugihara commented 2 years ago

Sorry, I cannot get your point... Even if you provide sorted and filtered bam files, QTL-seq check the quality and remove the improper paired reads, then sort the reads.

This error happened when your bam file doesn't exist. 1/ Please check whether qtlseq_output/20_bam/parent.unsorted.bam exits with a proper file size. 2/ Please check whether your input bam files can be opened by samtools view or not. samtools view a93.our_sm.sorted.rmdup.bam samtools view F1.our_sm.sorted.rmdup.bam samtools view F6.our_sm.sorted.rmdup.bam

They do not have path from your working directly?

Best, Yu Sugihara

Deeptirao commented 2 years ago

I have checked my bam files, which seem fine. Please see the two files attached and help me.

On Sat, Jun 25, 2022 at 7:48 PM Yu Sugihara @.***> wrote:

Sorry, I cannot get your point... Even if you provide sorted and filtered bam files, QTL-seq check the quality and remove the improper paired reads, then sort the reads.

This error happened when your bam file doesn't exist. 1/ Please check whether qtlseq_output/20_bam/parent.unsorted.bam exits with a proper file size. 2/ Please check whether your input bam files can be opened by samtools view or not. samtools view a93.our_sm.sorted.rmdup.bam samtools view F1.our_sm.sorted.rmdup.bam samtools view F6.our_sm.sorted.rmdup.bam

They do not have path from your working directly?

Best, Yu Sugihara

— Reply to this email directly, view it on GitHub https://github.com/YuSugihara/QTL-seq/issues/34#issuecomment-1166297267, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIDZKZ7ETAJDABNI2SOELSDVQ4ILZANCNFSM5ZXRVXSA . You are receiving this because you authored the thread.Message ID: @.***>

-- Regards,

Deepti Graduate Student, CCMB

YuSugihara commented 2 years ago

I cannot see your attached files.

If your BAM files are fine, would you try to run QTL-seq with full path?