ch4rr0
commented
1 week ago that is odd. I tried the version in question and it works for me.
$ ./bowtie2-align-s -x example/index/lambda_virus example/reads/longreads.fq | head
@HD VN:1.0 SO:unsorted
@SQ SN:gi|9626243|ref|NC_001416.1| LN:48502
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"./bowtie2-align-s -x example/index/lambda_virus example/reads/longreads.fq"
r1 16 gi|9626243|ref|NC_001416.1| 12259 42 194M * 0 0 GGGCCGCCATTGATGCGAAAAGCCGGGGGCTGACTGACCGGCAGGCAGAACGGGAAGCCACGGAACAGCGCCTGAAGGAACAGTATGGCGATAATCCGCTGGCGCTGAATAACGTCGTGTCAGAGCAGAAAAAGACCTGGGCGGCTGAAGACCAGCTTCGCGGGAACTGGATGGCAGGCCTGAAGTCCGGCTGG 8+25;+39E.:<73=(@*.6AH0;>1%20$EH/-.4A<.1-F8:<:1>A029F3";&AE#**E6;H5@2)-+B.7,49AF#,,",B!959=-1.E-&0%(@=&AB19A03))@+6/44D&?")>!6B#2=C,612/7,=+8,A&14+$&,(B66*(BDH79$"27!3<H=A4/71)4:)0>4/*>-@3,E%&%7 AS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:116A77 YT:Z:UU
r2 0 gi|9626243|ref|NC_001416.1| 15516 42 313M * 0 0 AAGCAGTAAGGGGCATACCCCGCGCGAAGCGAAGGACAACCTGAAGTCCACGCAGTTGCTGAGTGTGATCGATGCCATCAGCGAAGGGCCGATTGAAGGTCCGGTGGATGGCTTAAAAAGCGTGCTGCTGAACAGTACGCCGGTGCTGGACANTGAGGGNAATACCAACATATCCGGTGTCACGGTGGTGTTCCGGGCTGGTGAGCAGGAGCAGACTCCGCCGGAGGGATTTGAATCCTCCGGCTCCGAGACGGTGCTGGGTACGGAAGTGAAATATGACACGCCGATCACCCGCACCATTACGTCTGCAAAC 60./".G76C,0220H8@4B)"+&F2,0>$+%%%.&@><*%.=!!%G&$GB"+!*G)5<!;&!C?<(:7<<2'5?,<(?0.3)<?5%B@+6>G.B&B4D0D>D93B?H9"47!G$G50)AF(/A:005$*@,3>0F0'!3H<<B'/1!;+*3?&D3H%--HG*7,+#CH;.6)F!$4$FH;,?H:/-86!+7>93E,C1@,/.)H+8@C*(7/:4)*E2823.+>&EE/#A2A:*3>7(52@#,9-=@$$4)H,/F"9$!$EG%=0.@B>1@H7*+;682>@$D@/@(*6F2;66#AFBE4-45E*04-6=75 AS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:152C6G153 YT:Z:UU
Not sure if this is a known issue, but I've run into a bug where the output SAM from Bowtie2 does not fill the "VN:" field of the
@PGline:@PG ID:bowtie2 PN:bowtie2 VN: CL:"/opt/conda/bin/bowtie2-align-s...This seems like a minor issue, but it causes the ValidateSamFile command from Picard to throw the error "ERROR::POORLY_FORMATTED_HEADER_TAG", which precludes further analysis with the GATK pipeline.
I've been able to fix the header using samtools reheader, but it seems like ideally this should not be necessary.
Version 2.4.1
Cheers