Exec format error in unmapped bam file
Hello
I created unmapped bam file from fastq file (sample 1). When I tried to search the bam file using query name, I got the ‘Exec format error’
#1_ucheck.bam: unmapped bam file from Sample 1 fastq file
code: samtools view 1_ucheck.bam | grep 'A00684:110:H2TYCDMXY:1:1101:2790:1000'
Error: [E::hts_hopen] Failed to open file 1_ucheck.bam
[E::hts_open_format] Failed to open file "1_ucheck.bam" : Exec format error
samtools view: failed to open "1_ucheck.bam" for reading: Exec format error
I am not sure about this error. Because from the same fastq file (sample 1), could also align with reference sequence and convert it into a bam file. When I tried to search using queryname in this bam file, it did not show any error. It would be helpful, if someone could help to understand the error in the unmapped bam file. Thanks
#alignedsample1.bam: mapped bam file from sample1 fastq file
code: samtools view alignedsample1.bam | grep 'A00684:110:H2TYCDMXY:1:1101:2790:1000'
output: A00684:110:H2TYCDMXY:1:1101:2790:1000 99 NC_000012.12 10166659 60 101M = 10166871 313 TGATTGGACAGAAAGCTTCCACTATGTCTCCTTACCCACCCTTCTCCCAATACCTGAACAATTTGCTACTCTCTTCAGTGTTTCTTGGAGATTCAGATTCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFF:: NM:i:0 MD:Z:101 MC:Z:101M AS:i:101 XS:i:0
A00684:110:H2TYCDMXY:1:1101:2790:1000 147 NC_000012.12 10166871 60 101M = 10166659 -313 GCCGGGCTGAGATCTGTCCCTCCAGTTTCTTTTTCTGGTGAGTTAGGTTTGCTTGCTCTTGTGTTAGGAGGTCAGACACCTGGGATACTGAATCACAGTTG FFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:101 MC:Z:101M AS:i:101 XS:i:20
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