Error in SAM format

I trying to create alignment in the SAM format by using the following command

bwa samse genome.fa Seq1.bwa Seq1.fastq > Seq1_se.sam

After 5min I got the following error message

[bwa_aln_core] convert to sequence coordinate... Killed

sam aln bwa samse

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written 4.6 years ago by NM 0

how much memory do you have on your machine ?

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written 4.6 years ago by Pierre Lindenbaum 17K

I have 8GB of memory.

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written 4.6 years ago by NM 0

and available 2.98 GB

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written 4.6 years ago by NM 0

That is likely not enough. What genome are you working with?

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written 4.6 years ago by GenoMax 16K

human genome

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written 4.6 years ago by NM 0

I am afraid you may be able to use bwa as long as nothing else was running. Otherwise you may want to try subread. Most other aligners are not going to work.

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written 4.6 years ago by GenoMax 16K

Thank you

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written 4.6 years ago by NM 0

0 answers

No answers yet.

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