Doing nohup samtools sort and [ 1]+ Exit 1 is showing up
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10 months ago

I'm currently trying to run a samtools sort on some bam files nohup samtools sort sample.bam s0rted.bam & and I keep on getting [ 1]+ Exit 1 nohup samtools sort sample.bam s0rted.bam when I press enter Why is this happening and how do I fix this problem?

I'm trying to sort the file to index it!

samtools unix alignment command line index • 384 views
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I personally dislike the habit of nohuping and sending processes to background. Either use a batch system if you are on a cluster or use something like GNU screen to be able to log in- and out of processes without the need to have a terminal open. Beyond that maybe your command is wrong, the syntax for sort you use is very old, what is the output of samtools --version?

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If I'm not wrong nohup prints a log file called nohup.out. What is the output/content of this file?

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10 months ago
aw7 ▴ 40

Your syntax is wrong. All your command will be doing is printing out usage. You want something like:

samtools sort sample.bam -o s0rted.bam
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