[Samtools-help] Tag lost during samtools sort

[Mark R. <mra...@ni...>]

Hello all,

When running samtools sort to sort a large number of bam files using the following line:

> samtools sort -T sorting -O bam -o $outfile $infile


I get the following error messages printed to the screen:

> [bam_sort_core] merging from 2 files...
> [bam_translate] PG tag "A" on read "1_1101_10360_49339_1" encountered with no corresponding entry in header, tag lost

The number of reads appears to remain the same between the sorted/unsorted bams. Can anyone give any insight into what this means?

Many thanks

Mark
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Mark Ravinet
Postdoctoral Research Fellow
Ecological Genetics Laboratory
National Institute of Genetics
Yata 1111, Mishima, Shizuoka
411-8540, Japan
Email: mra...@ni...
Skype: mark.ravinet
+44 (0) 7841 67 58 63 (UK)
+81 (0) 90 7211 3590 (Japan)
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