Hi Peter, Thanks for your reply.
Grepped lines from a typical header are as follows: > @PG ID:GSNAP PN:gsnap VN:2013-11-27 CL:gsnap -d stick_ref > --maxsearch=10 -M 0 -m 5 -t 6 -n 1 -A sam --quiet-if-excessive > --terminal-threshold=10 -i 2 ./samples_081014/CHA13_N_PA_F.fq > Similarly, the grepped line of one of the entry errors is as follows: > 1_1101_10360_49339_1 16 groupI 11728 40 90M * 0 > 0 > TCAATTATATTTAATATGAATAGTTACACCGTTAAACCAGCGTTGCATTTTTCCTCTCAAGGAATCCCTAGAGCCGCTTGCGTGCCTGCA > > C>DCDDCDCAEDDDEDEEECDCCA>BA?DDDDCBA?CADFFHFFEHGIIGIGJJJIGFIHHCIJIIHGHFJJJIJIIJJIGGFFCCIHFH > MD:Z:90 NH:i:1 HI:i:1 NM:i:0 SM:i:40 XQ:i:40 X2:i:0 XO:Z:UU PG:Z:A I guess the error seems to have something to do with the “A” tag at the end of the entry? However I ran these commands on a group of bams including several which do not produce this error and they also have the “A” tag and an identical header. Here is an example which produces no errors: > @PG ID:GSNAP PN:gsnap VN:2013-11-27 CL:gsnap -d stick_ref > --maxsearch=10 -M 0 -m 5 -t 6 -n 1 -A sam --quiet-if-excessive > --terminal-threshold=10 -i 2 ./samples_081014/CHA117_N_PA_F.fq And a typical read: > 1_1101_19655_2193_1 0 groupXX 10637098 40 90M * > 0 0 > TGCAGGAGAAAGATAGTGGACTAACTATGCCCCACACGCTACACACTCACACATCCTACACCACATAGTTGCACTAATAATTTGCATGTT > > HHHIGG<BFHHG99BF2<?*1?B<99C4?4DBFHBHGIIIC8FFCA;=7@77?EDEDDCD;>AC;;@>(-;CCC>>:5@>A######### > MD:Z:90 NH:i:1 HI:i:1 NM:i:SM:i:40 XQ:i:40 X2:i:0 XO:Z:UU PG:Z:A Thanks for your help so far! Mark > On 5 Nov 2014, at 19:31, Peter Cock <p.j.a.c...@googlemail.com> wrote: > > Hi Mark, > > The error message comes from function bam_translate in bam_sort.c, > where it attempts to update the read's PG tag. Apparently the PG > tag does not match any of the @PG entries in your header: > https://github.com/samtools/samtools/blob/develop/bam_sort.c > > Can you share the output of: > > $ samtools view -H your_file.bam > > If that is very long, at least show us the @PG lines: > > $ samtools view -H your_file.bam | grep "^@PG" > > And the entry/entries for the read giving the error: > > $ samtools view your_file.bam | grep "^1_1101_10360_49339_1" > > Regards, > > Peter > > > On Wed, Nov 5, 2014 at 8:39 AM, Mark Ravinet <mravi...@nig.ac.jp> wrote: >> Hi Peter, >> >> Apologies, I should have mentioned that in my last email. It was samtools 1.0 >> >> Thanks >> >> Mark >> >>> On 5 Nov 2014, at 17:34, Peter Cock <p.j.a.c...@googlemail.com> wrote: >>> >>> Hi Mark, >>> >>> Which version of samtools was this? >>> >>> Peter >>> >>> On Wed, Nov 5, 2014 at 3:44 AM, Mark Ravinet <mravi...@nig.ac.jp> wrote: >>>> 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 >>>> ------------------------------------------------ >>>> Mark Ravinet >>>> Postdoctoral Research Fellow >>>> Ecological Genetics Laboratory >>>> National Institute of Genetics >>>> Yata 1111, Mishima, Shizuoka >>>> 411-8540, Japan >>>> Email: mravi...@nig.ac.jp >>>> Skype: mark.ravinet >>>> +44 (0) 7841 67 58 63 (UK) >>>> +81 (0) 90 7211 3590 (Japan) >>>> ------------------------------------------------ >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Samtools-help mailing list >>>> Samtools-help@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/samtools-help >>>> >> ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
