The bioBakery help forum

"Unable to read file magic number" error

Hello,
I’m trying to run kneaddata on whole metatranscriptome sequencing files, similarly to how it outlined in the wmgx_wmtx biobakery workflow. Kneaddata is working on some files, but not all. It crashes when it gets to the kneaddata_bowtie2_discordant_pairs step. I consistently get the same error:

kneaddata.utilities - DEBUG: b'Unable to read file magic number\nUnable to read file magic number\nUnable to read file magic number\nUnable to read file magic number\n0 reads\n0.00% overall alignment rate\npair1_aligned : 0\npair2_aligned : 0\npair1_unaligned : 0\npair2_unaligned : 0\norphan1_aligned : 0\norphan2_aligned : 0\norphan1_unaligned : 0\norphan2_unaligned : 0\n'

Any help resolving this issue would be greatly appreciated!

Mark

Hi @Mark_Young,

Do you mind posting the input sequence headers please? One of the reason for this issue might be that sequence headers are not formatted right.

Regards,
Sagun