some unrelated info in SAM file generated by BWA

Question

[zhangdengwei]

hi,

I found there is an unrelated row, not the header, existing in my SAM file, which produced by BWA mem. like the error below ([M::process] read 397352 sequences (120000304 bp)...[M::mem_process_seqs] Processed 397352 reads in 815.105 CPU sec, 67.779 real sec):

SRR5439471.393892       0       chr3    25046051        60      147M155S        *       0       0       ATCATGTAGTCTGCCCGGCTCTTTTGGTCCTAGATCAGAAAGAGGCTTTTGCAAACCCACCATTTCTGGGGTTGAATGGGAAATTAGGGAAAGAAAATGAGGTCAAGAAAGGCATGGAGAAAAAAACCGCTGGGCCTGTTGGCCTGAACGGTTCTTGAGAACTGCCATCACTTGTAGCTTCAAATCAGCTGCCAAAAATAGTGGAAAGACTAATTGTTATTTCAGGTATAAAGAAACAGCAACGGTGGACCGATGATCATCGGTCCACCGTGAACTGCCTGAGTTACTTGTCCCTGCCTCTG  HHHHHHHHGGGGGGGGHHHEHHHEHHHHGHHHHHHGHHHHHHHHHEFEHHHGGFAGEFGGHHFHHGGGGHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHGGGGGEEGGHGFGGGGCGGCBBFFFFFBABBBBBBBBFF4AFFFGGGGGGGGGGHHHHHHHGGHHHHHHHBGHGHHGHGHHHHHHBGHHHHHHHFFHHHHHHHHHGGHHHHGHHGHFHHHHHHHEGEGFHHHGGGGGEFHGHEFEEGHHHGHGGGHBFHHHF2FGHHHHHHHHHHHHHHHHHF  NM:i:0  MD:Z:147        AS:i:147        XS:i:0  SA:Z:chr1,183484475,-,61S90M151S,60,0;chr2,171679085,+,271S31M,60,0;
SRR5439471.393892       2064    chr1    183484475       60      61H90M151H      *       0       0       TGCTGTTTCTTTATACCTGAAATAACAATTAGTCTTTCCACTATTTTTGGCAGCTGATTTGAAGCTACAAGTGATGGCAGTTCTCAAGAA      HHHHHFHGHHGHHHHGGHHHHHHHHHFFHHHHHHHGBHHHHHHGHGHHGHGBHHHHHHHGGHHHHHHHGGGGGGGGGGFFFA4FFBBBBB      NM:i:0  MD:Z:90 AS:i:90 XS:i:19 SA:Z:chr3,25046051,+,147M155S,60,0;chr2,171679085,+,271S31M,60,0;
SRR5439471.393892       2048    chr2    171679085       60      271H31M *       0       0       GAACTGCCTGAGTTACTTGTCCCTG
[M::process] read 397352 sequences (120000304 bp)...[M::mem_process_seqs] Processed 397352 reads in 815.105 CPU sec, 67.779 real sec
CCTCTG  GGGHBFHHHF2FGHHHHHHHHHHHHHHHHHF NM:i:0  MD:Z:31 AS:i:31 XS:i:0  SA:Z:chr3,25046051,+,147M155S,60,0;chr1,183484475,-,61S90M151S,60,0;
SRR5439471.393893       16      chr3    25046051        60      151M151S        *       0       0       ATCATGTAGTCTGCCCGGCTCTTTTGGTCCTAGATCAGAAAGAGGCTTTTGCAAACCCACCATTTCTGGGGTTGAATGGGAAATTAGGGAAAGAAAATGAGGTCAAGAAAGGCATGGAGAAAAAAACCGCTGGGCCTGTTGGCCTGAGCACGCCAACCACCCACCTCGGTCTCCCAAAGGGCTGGAACGGTGGACCGATGATCATCGGTCCACCGTTCTGTTACTTAGGGAAATTACAAGCATATTAAGTTCAGCTGCCTTAGCAAAGCTTCAGAACTTCTTAAGGTTTAATATTTTTATTA  FEGHHGHHHEGGGGGGHHEGGEHHGGGBHHFHHHHGHHGHHHHHG3HHHHHGGGGGGFHHHHHFGGGGGHHHHHHHHHHHHHHHHGGHHHHHHHGHHHHHHGHHHHHHHHHHGHHHHHHGGGGGGEGGHGGGGGGGGGGCBFF4FFAABBBABCCCCCCCCCCGGGGGGGGGGHHHHHHFGGHGGHHHFGBFFGHHGGGGHHHHHHHGGGGHHHGGEHGHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHGHHHHHHHHHHHHHHHGHHG  NM:i:0  MD:Z:151        AS:i:151        XS:i:0  SA:Z:chr3,25045723,-,216S86M,60,0;chr4,169910618,+,115S36M151S,37,0;
SRR5439471.393893       2064    chr3    25045723        60      216H86M *       0       0       TCTGTTACTTAGGGAAATTACAAGCATATTAAGTTCAGCTGCCTTAGCAAAGCTTCAGAACTTCTTAAGGTTTAATATTTTTATTA  EHGHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHGHHHHHHHHHHHHHHHGHHG  NM:i:0  MD:Z:86 AS:i:86 XS:i:20 SA:Z:chr3,25046051,-,151M151S,60,0;chr4,169910618,+,115S36M151S,37,0;*

And my alignment command is

nohup bwa mem -t 12 GRCh38.bwa VEGFA_site_1.fastq.gz > VEGFA_site_1_output.sam &

Was my command incorrect? Thanks for your help!!!

Answer 1

[WouterDeCoster]

Well, there is your problem. If you use nohup then STDOUT and STDERR get combined in the output file. Either don't use nohup or use the -o option as mentioned by Bastien Hervé

Answer 2

[Bastien Hervé]

Please use the option -o to output your sam file and not redirecting to standard output using >. In your case you have BWA verbose in your sam file, caused by redirection

bwa mem -t 12 GRCh38.bwa VEGFA_site_1.fastq.gz -o VEGFA_site_1_output.sam

[zhangdengwei]

Sorry, my version of BWA is 0.7.12-r1039, and there is no -o option. Did we use the same version?

[Bastien Hervé]

I have this one Version: 0.7.17-r1188

-o FILE       sam file to output results to [stdout]

Answer 3

[GokalpC]

If you must use nohup and there is no -o FILE option call bwa from an inner bash call.

nohup bash -c 'bwa mem -t 12 GRCh38.bwa VEGFA_site_1.fastq.gz > VEGFA_site_1_output.sam' &

That should take care improper redirection of stdout.