I would like to convert a bowtie2 generated .sam file to .bam with samtools (v1.9) but I get truncated files with SEQ and QUAL of different lenghts. The error line SEQ and QUAL's are indeed of different lenght but I don't know how to fix this.Why am I getting this error?
$ samtools view -b hiPSC1.sam > hiPSC1.bam
[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] Parse error at line 8272508
[main_samview] truncated file
here's how my .sam file looks:
@SQ SN:chrY LN:57227415
SRR2097503.1.3 83 chrM 6842 1 51M = 6745 -148 TATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAG >>?8/:AA6A@?0DB9DB<?B@A@<DDC?)1EEC=CA?A+D?DDD@;D??? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:51 YS:i:0 YT:Z:CP
and here is the line giving me the error:
$ sed -n 8272508p hiPSC1.sam
SRR2097503.1.4850276 99 chrM 14650 34 51M = 14804 205 CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC CCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJIGGDJIJJIGJHHHHHFFFFFCCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:51 YS:i:0 YT:Z:C
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written
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meilinfer •
It's a problem with your SAM, not with samtools. It looks like a problem in your upstream process and you should not trust this data.
You can always filter out the bad lines with awk....
awk -F '\t' '$0 ~ /^@/ || length($10)==length($11)' input.sam
It worked!! I checked the file with:
samtools quickcheck -v
and it was okay and was even able to sort the file.Thanks!
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Please go back and check your original data file to see if the problem exists there as well.
The SAM file is corrupted. Maybe an issue during alignment, amybe out-of-memory at some point. I would realign everything from scratch. If it is only this one read then you can also remove it and see if that fixes it. I would still realign:
which will produce a BAM file right away without intermediate sam files. This is called a Unix
pipe.Thanks AT point I used bowtie2 to align and use a prebuilt index I downloaded from Bowtie's webpage. I'll try realigning again and piping samtools
You could use a pipe as suggested by @ATPoint or use the correct option to create the SAM file instead of the redirect you used.
I did not use the -S!! Thanks I'll give it a go and align again. Thanks.