Closed Deeptirao closed 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
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
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Deepti Graduate Student, CCMB
I cannot see your attached files.
If your BAM files are fine, would you try to run QTL-seq with full path?
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