Question: Samtools Sort
0
gravatar for GPR
7.1 years ago by
GPR320
Mexico
GPR320 wrote:

Hello, I am trying to sort a large bam file, actually split in two, with samtools sort I use -m 10000000000 so the job creates 8 sorted files of about the same size, plus a smaller last one. At the end of the job, samtools sort give the message "coresortmerge 9 bam files" and it stays like that for a while before the screen starts showing multiple caracters one after the other.

My question is, can I assume the job was completed? My command-line was

samtools sort -no -m 10000000000 inpunt.bam output.prefix &

Any help appreciated.

deleted-post • 5.1k views
ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by GPR320
2
gravatar for Istvan Albert
7.1 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

You are using the -o flag, this will output the file to the standard output. What you are seeing is the bam file. Don't add the flag, or if you do redirect the output.

ADD COMMENTlink written 7.1 years ago by Istvan Albert ♦♦ 80k
0
gravatar for GPR
7.1 years ago by
GPR320
Mexico
GPR320 wrote:

I need to have a STDOUT, in order to use the sorted bam to create an mrf (RSEQ tools). So you recommend redirecting the output ( > output) in order to get a single bamfile output? I guess I can always merge the multiple bam files. What am worried about is whether or not the job finished successfully. Especially because the last file is smaller that the other ones, and because no "done" message appears.

Thanks for helping!

ADD COMMENTlink written 7.1 years ago by GPR320
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