I generated a de novo assembly of illumina hiseq reads using Abyss & trans-Abyss, aligned the reads back to the assembly using bowtie2, and am now trying to view the resulting SAM alignment in IGV. IGV recommends BAM over SAM, but I'm getting errors in converting to BAM using samtools.
The command I'm using is:
Though I get a resulting bam file, I also get this output in my terminal:
When I ignored the error and tried to sort the bam file with the command:
I got the error:
Here are the first few lines of my SAM file:
@HD VN:1.0 SO:unsorted
@SQ SN:k48:100000u LN:120
@SQ SN:k48:100008 LN:199
@SQ SN:k48:100019u LN:95
@SQ SN:k48:100020 LN:195
Can anyone help? I haven't been able to find relevant help on seqanswers or anywhere else.
The command I'm using is:
Code:
samtools view -bhS Ua_1.0_pn.sam > Ua_1.0_pn.bam
[samopen] SAM header is present: 200079 sequences.
[sam_read1] reference '323' is recognized as '*'.
Parse error at line 60897629: sequence and quality are inconsistent
Abort trap
[sam_read1] reference '323' is recognized as '*'.
Parse error at line 60897629: sequence and quality are inconsistent
Abort trap
Code:
samtools sort Ua_1.0_pn.bam Ua_1.0_pn_sort.bam
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_sort_core] truncated file. Continue anyway.
Bus error
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_sort_core] truncated file. Continue anyway.
Bus error
@HD VN:1.0 SO:unsorted
@SQ SN:k48:100000u LN:120
@SQ SN:k48:100008 LN:199
@SQ SN:k48:100019u LN:95
@SQ SN:k48:100020 LN:195
Can anyone help? I haven't been able to find relevant help on seqanswers or anywhere else.
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