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songweizhi / MarkerMAG

Linking MAGs with 16S rRNA marker genes
GNU Affero General Public License v3.0
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sorted_sam16s error #1

Closed ajcardenasb closed 3 years ago

ajcardenasb commented 3 years ago

Hello,

Thanks you for developing MarkerMAG, the tool looks really promising!

I'm having the following error every time I try to run MarkerMAG link.

Traceback (most recent call last): File "/home/cardena/miniconda3/bin/MarkerMAG", line 126, in link_16s.link_16s(args) File "/home/cardena/miniconda3/lib/python3.7/site-packages/MarkerMAG/link_16s.py", line 2703, in link_16s reads_vs_16s_sam = args['sorted_sam16s'] KeyError: 'sorted_sam16s'

The command I'm using is:

MarkerMAG link -p sponges_markerMAG_output -r1 sponge_R1.fasta -r2 sponge_R2.fasta -marker interesing_bacteria.fasta -mag ./binning/chosen_bins -x fa -t 64 -tmp -force

I tried with and without renaming fasta files using "MarkerMAG rename_reads" but I always get to the same error.
Am I missing something?

Thanks for clarification! Anny

songweizhi commented 3 years ago

Thanks for your interest in using MarkerMAG, Anny. This issue has been fixed in the latest version (v1.0.41). Best, Weizhi

ajcardenasb commented 3 years ago

Thank you, Weizhi! I'll try it out