[W::sam_parse1] urecognized reference name; treated as unmapped

Question

[Quak]

Basically, when I am trying to convert SAM files generated from SOAP2 aligner (the same is directly generated from soap2sam.pl script privided by SOAP developers), I am encountering

[W::sam_parse1] urecognized reference name; treated as unmapped

warning!

Has anyone face the same problem ? I couldn't find much advises on google - so decided to open a post here!

Answer 1

[Devon Ryan]

This will happen whenever you have a read mapping to a chromosome/contig that's not in the header (and a header is present with at least one chromosome/contig listed). What's the header of the SAM file look like?

[somon_955]

Hi, I have a similar problem when I try to convert the SAM file from the aligner to BAM file.

Following are some lines from the file. I do not see any obvious problem with the header assignment (but then, I have started working on NGS data only recently).

@HD VN:1.0 SO:coordinate

@SQ SN:gi|556503834|ref|NC_000913.3| LN:4641652

SRR1948068.45070 99 gi|556503834|ref|NC_000913.3| 1217250 160 251= * 0 0 ACCATGCTCTCTGTAGATGCCAGCGCGAGCGAATGAATGGCATTTTCATGTATTAAACCCTTTGGCCGGGACAAGCAAATGCGCAATACACTCATACCCATCCTCGTTGCGATATGCTTGTTTATTACCGGTGTCGCTATTTTGAACATCCAGCTCTGGTATTCCGCAAAAGCAGAGTACCTGGCGGGAGCGAGATATGCCGCCAACAATATCAATCATATACTTGAAGAAGCGTCACAAGCGACTCAAAC CCCCCFFFFFFFGGGGGGGGGGHGGGGGGGGGGGHHHHHGHHHHHHHHHHFHHHHHHHHGHHHHGHHGGGGGGHHHHHHHHHGGGGGHHGHHHHGHHHHHHHHHHGHGHGGGGGGHHHHHHGHHHHHHHGGGGGHGHGGGHHHHGHHHHHHHHHHHHGHHHHHHHHGGGGHHHGHHGHHHHHGHGGAGGFFFFFFFFFFFFFDAFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFDFDAFFFFFFFFFFBF0

Could someone please help me locate what the problem is?