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5.3 years ago
priya120195
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20
After converting sam file into bam file I was using the below command to get unmapped file
samtools view -b -f 12 sample_mapped_and_unmapped.bam > sample_bothEndsUnmapped.bam
This command is not showing error but its getting stopped within seconds by creating a very small size file which on doing head sample_bothEndsUnmapped.bam saying that error in line 1, truncated file. I am showing here the head and tail od my sam an bam files ,so that the error can be resolved. head bam:below
[W::sam_hdr_parse] duplicated sequence 'BDDB'
[W::sam_hdr_parse] duplicated sequence 'BDB'
[W::sam_hdr_parse] duplicated sequence ':'
[W::sam_hdr_parse] duplicated sequence 'B'
[W::sam_hdr_parse] duplicated sequence '4'
[W::sam_hdr_parse] duplicated sequence '<'
[W::sam_hdr_parse] duplicated sequence '<'
[W::sam_hdr_parse] duplicated sequence 'B'
[W::sam_hdr_parse] duplicated sequence ':'
[W::sam_hdr_parse] duplicated sequence 'C'
[W::sam_hdr_parse] duplicated sequence '4'
[W::sam_hdr_parse] duplicated sequence 'A@'
[W::sam_hdr_parse] duplicated sequence ':'
[W::sam_hdr_parse] duplicated sequence '<'
[W::sam_hdr_parse] duplicated sequence '@'
[W::sam_hdr_parse] duplicated sequence 'CC'
[W::sam_hdr_parse] duplicated sequence 'A'
[W::sam_hdr_parse] duplicated sequence 'B'
[W::sam_hdr_parse] duplicated sequence 'A'
[W::sam_hdr_parse] duplicated sequence 'A'
[W::sam_hdr_parse] duplicated sequence 'C'
[W::sam_hdr_parse] duplicated sequence 'C>'
[W::sam_hdr_parse] duplicated sequence '5'
[W::sam_hdr_parse] duplicated sequence 'B'
[W::sam_hdr_parse] duplicated sequence 'C'
[W::sam_hdr_parse] duplicated sequence 'C'
[W::sam_hdr_parse] duplicated sequence '5'
[W::sam_hdr_parse] duplicated sequence 'BB'
[W::sam_hdr_parse] duplicated sequence 'C>'
[W::sam_hdr_parse] duplicated sequence '5'
[W::sam_hdr_parse] duplicated sequence 'ACC'
[W::sam_hdr_parse] duplicated sequence 'C'
[W::sam_hdr_parse] duplicated sequence 'A@'
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head sam: below
@HD VN:1.0 SO:unsorted
@SQ SN:NC_000001.11 LN:248956422
@SQ SN:NT_187361.1 LN:175055
@SQ SN:NT_187362.1 LN:32032
@SQ SN:NT_187363.1 LN:127682
@SQ SN:NT_187364.1 LN:66860
@SQ SN:NT_187365.1 LN:40176
@SQ SN:NT_187366.1 LN:42210
@SQ SN:NT_187367.1 LN:176043
@SQ SN:NT_187368.1 LN:40745
@SQ SN:NT_187369.1 LN:41717
@SQ SN:NC_000002.12 LN:242193529
@SQ SN:NT_187370.1 LN:161471
@SQ SN:NT_187371.1 LN:153799
@SQ SN:NC_000003.12 LN:198295559
@SQ SN:NT_167215.1 LN:155397
@SQ SN:NC_000004.12 LN:190214555
@SQ SN:NT_113793.3 LN:209709
@SQ SN:NC_000005.10 LN:181538259
@SQ SN:NT_113948.1 LN:92689
@SQ SN:NC_000006.12 LN:170805979
@SQ SN:NC_000007.14 LN:159345973
@SQ SN:NC_000008.11 LN:145138636
@SQ SN:NC_000009.12 LN:138394717
please resolve the issue.
what is the version of samtools ?
what is the output of the following command
Samtools version 1.4
Currently I am on leave. You are requested to kindly wait for a week or till 14 so that I can reply to the next part of the question.
Please avoid phrases such as "please resolve the issue" or "wait for a few days". Such time/urgency related statements do not come across as professional on a forum.
The ouput of the command
is
Please tell what this output signify? Is there any issue with bam file?
this is NOT a bam file. The output of file sample _mapped and unmapped. bam shouldn't be
databut:gzip compressed data, extra fieldorBAM file version...I tried with all my samples, but still I am struggling with same issue. All the commands are running perfectly ,even the bam file generated is having size in Gb but why I am lacking i am not getting. Even other people of my lab are running the same tool and they are not facing this issue .
Please help me in resolving my query