Dear SAMtools community,
I am trying to view the contents of a SAM file using “samtools view”, but
unfortunately it fails with the following error message: [W::sam_parse1]
urecognized reference name; treated as unmapped
I need to use SAMtools to calculate the statistics and subsequently convert the
SAM file to BAM.
My first guess was that the chromosome name is not present in the header for
whatever reason. However, if I open the SAM file with the text viewer (e.g.
less), I see that all chromosomes are there:
@HD VN:1.0 SO:unsorted
@SQ SN:chr1 LN:2955898172
@SQ SN:chr2 LN:2923849100
@SQ SN:chr3 LN:2495613285
@SQ SN:chr4 LN:2453368029
@SQ SN:chr5 LN:2630329465
@SQ SN:chr6 LN:3136375085
@SQ SN:chr7 LN:2029504283
@SQ SN:chr8 LN:1710882196
@SQ SN:chr9 LN:1495491496
@SQ SN:chr10 LN:1639492812
@SQ SN:chr11 LN:1436510532
@SQ SN:chr12 LN:1210869585
@SQ SN:chr13 LN:718908455
@SQ SN:chr14 LN:657912494
I assume that the error occurs because the lengths of the first 6 chromosomes
are longer than 2^31 bp. Those are the ones that generate the error messages in
the “samtools view” output. Chromosomes 7-14 are present in the output.
Is this assumption correct?
Is there an easy fix for this issue? I would prefer not to split the
chromosomes into p and q arms at this point. However, I might have to do so if
there is no other way.
SAMtools version is 1.9 (I also tried 1.4 and 1.6).
Thanks a lot!
Best regards,
Sergej
Dr. Sergej Nowoshilow
Post-doc in Tanaka Lab
Elly Tanaka group
Animal models of regeneration
Campus-Vienna-Biocenter 1
1030 Vienna
email: sergej.nowoshi...@imp.ac.at
phone: +43 (0) 1 79730 3203
orcid: 0000-0001-8360-5010<https://orcid.org/0000-0001-8360-5010>
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