The SAM has the header split, with query 1 and 2 headers and alignments appearing concatenated, rather than correctly combined headers.
I cannot identify why this example causes this issue, and I would appreciate some guidance on how to resolve it or if there are some issues with the tools/commands.
Hi,
I have an issue with SAM file header formatting. The input FASTA contains two queries, and the blastn_vdb search is against one SRA accession.
After running (example)...
and...
The SAM has the header split, with query 1 and 2 headers and alignments appearing concatenated, rather than correctly combined headers.
I cannot identify why this example causes this issue, and I would appreciate some guidance on how to resolve it or if there are some issues with the tools/commands.
Many thanks
ASN.asn.gz bad_formatted.sam.gz input.fasta.gz