parent.unsorted.bam not found

[Brent-Saylor-Canopy]

Hi,

I am trying to run your pipeline from bam files.

I use the launch command:

qtlseq -r ref.fasta \
       -t 30 \
      -p  /20_bam/parent.bam \
      -b1 /20_bam/bulk1.bam \
      -b2 /20_bam/bulk2.bam \
      -n1 38 \
      -n2 38 \
      -o ../out

However I get the following error:

QTL-seq:2021-05-03 11:36:27] start to run QTL-seq.
[QTL-seq:2021-05-03 11:36:27] maximum number of threads which you can use is up to 32.
[QTL-seq:2021-05-03 11:36:27] start to index reference fasta.
[QTL-seq:2021-05-03 11:52:37] indexing of reference successfully finished.
[QTL-seq:2021-05-03 11:52:37] start to merge BAMs.
[QTL-seq:2021-05-03 11:52:37] !!ERROR!! samtools sort -m 1G -@ 30 -o ../out/20_bam/parent.bam 
../out/20_bam/parent.unsorted.bam >> 
../out/log/samtools.log 2>&1

please check below:
[E::hts_open_format] Failed to open file "
../out/20_bam/parent.unsorted.bam" : No such file or directory
samtools sort: can't open "../out/20_bam/parent.unsorted.bam": No such file or directory

Is parent.unsorted.bam something I was supposed to generate?

[YuSugihara]

Sorry for my late reply.

Probably, you should set not "../out" but "out" using the option "-o" . Please try.

And, I also want to ask which version of QTL-seq are you using?

[Brent-Saylor-Canopy]

Thanks, that was the issue