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Question: samtools sort: truncated file. Aborting
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gravatar for m.t.lorenc
22 months ago by
m.t.lorenc • 0
m.t.lorenc • 0 wrote:

Hi, I got an error by using this the below command:

samtools sort -O SAM -n -@ 2 -o OZBenth2_.fastp.fq.gz.name-sorted.sam OZBenth2_.fastp.fq.gz.sam 
[W::sam_read1] Parse error at line 1
samtools sort: truncated file. Aborting

What did I miss?

Thank you in advance,
samtools picard alignment • 1.4k views
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modified 22 months ago • written 22 months ago by m.t.lorenc • 0
0
gravatar for lakhujanivijay
22 months ago by
lakhujanivijay ♦ 5.4k
India/Ahmedabad
lakhujanivijay ♦ 5.4k wrote:

Samtools expect a bam file and you have proivided a sam file (see usage below). 

Usage: samtools sort [options...] [in.bam]

So, first try converting sam to bam.

samtools view -bS OZBenth2_.fastp.fq.gz.sam > OZBenth2_.fastp.fq.gz.bam
ADD COMMENT • link written 22 months ago by lakhujanivijay ♦ 5.4k

Thank you, do you think java -jar picard.jar SortSam I=input.sam O=sorted.samSORT_ORDER=coordinat would be slower?

ADD REPLY • link written 22 months ago by m.t.lorenc • 0
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