SAM line does not contain at least 11 tab-delimited fields
I am not understanding what this error means i tried this command too but its showing me same error
samtools view -bf 1 1A_sorted.bam > 1A_Sorted.bam
Error occured when reading beginning of SAM/BAM file. ('SAM line does not contain at least 11 tab-delimited fields.', 'line 1 of file 1A_Sorted.bam') [Exception type: ValueError, raised in _HTSeq.pyx:1276]
samtools view 1A_sorted.bam | head
HWI-D00574:89:C6ABRANXX:2:1101:7450:50398 133 gi|448814763|ref|NC_000962.3| 1 0 * = 1 0 CAACAACGGTTGTAGCTCGACCCGGAACCAAGACCCGGAACTAACGAGAACCAGGCAGATACGTCGTTGACCGATGACCCCGGTTCAGGCTTCACCACAGT B3A?AGB//=/CFDFG11=/E/E9///<CFB:FGGB///<B<1DDGB//91:1000>/0<::0<CB/E00@C9/:C######################### YT:Z:UP
HWI-D00574:89:C6ABRANXX:2:1102:3006:26295 133 gi|448814763|ref|NC_000962.3| 1 0 * = 1 0 GGAACCAAGACCCGGAACTAACGAGAACCAGGGAGATACGTCGTTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAAC BBBBBGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBGGGGGG YT:Z:UP
HWI-D00574:89:C6ABRANXX:2:1102:12755:32164 163 gi|448814763|ref|NC_000962.3| 1 0 2M13I86M = 1 -97 GGGAGATACGTCGTTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGAC CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGBCCCGG AS:i:-54 XN:i:0 XM:i:2 XO:i:1 XG:i:13 NM:i:15 MD:Z:0T0T86 YS:i:-32YT:Z:CP
HWI-D00574:89:C6ABRANXX:2:1102:1302:32973 163 gi|448814763|ref|NC_000962.3| 1 23 2M13I86M = 19 119 GGGAGATACGTCGTTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACCCTAAGGTTGACGACGGAC B@BBB>G>DGDGGGGGFGGD<EGGGGG9CGGGGGGGGGGGGGGGGGGGGGGGD>GGGGG>CGGGGGGEDG<FGECGGGGGG;CGGGEDGGGB=ED68CDC: AS:i:-54 XN:i:0 XM:i:2 XO:i:1 XG:i:13 NM:i:15 MD:Z:0T0T86 YS:i:-3YT:Z:CP
HWI-D00574:89:C6ABRANXX:2:1102:6812:34459 133 gi|448814763|ref|NC_000962.3| 1 0 * = 1 0 CAACGGTTGTAGCTCGACCCGGAACCAAGACCCGGAACTAACGAGAACCAGGGAGATACGTCGTTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTG ABBBCGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGBGGGGGGGGGGGGGGGGGGGGGGGGGGGG YT:Z:UP
HWI-D00574:89:C6ABRANXX:2:1102:16322:88949 133 gi|448814763|ref|NC_000962.3| 1 0 * = 1 0 CAACAACGGTTGTAGCTCGACCCGGAACCAAGACCCGGAACTAACGAGAACCAGGGAGATACGTCGTTGACCGATGACCCCGGTTCAGGCTTCACCACAGT BBCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC YT:Z:UP
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This doesn't look like SAM/BAM format to me.
this is what i got after sorting and indexing the .bam file
At some point thing got corrupted, you might have to remake
1A_sorted.bam.this error solved:
i tried installing
Then
however still there is some problem because my htseq_1_file is of 0 byte. Nothing reported inside that file. It is full blank.
How have you created 1A_sorted.bam?
using command samtools sort 1A.bam 1A_sorted.bam
I'm also going to chime in and say this is a SAM format file that has been corrupted in a deeply confusing way. How was this file generated?
EDIT It looks like you've changed your example and now this looks like a SAM file. Glad you got this AHEM: ...sorted out :)
What mapping tool did you use?
i used Bowtie2........