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amandawarr / Lilo

Stitch together Nanopore tiled amplicon data without polishing a reference
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Error in rule reporechop: #2

Closed tboonf closed 2 years ago

tboonf commented 2 years ago

Hello, While running the sample dataset, I have encoutered the following error messages. I have made such that prochop is installed correctly and in the path.

Any help is greatly appreciated.

Error in rule reporechop: jobid: 2 output: FAT94769_pass_barcode02_66883b35_0/polished_trimmed.fa shell: porechop --adapter_threshold 72 --end_threshold 70 --end_size 30 --extra_end_trim 5 --min_trim_size 3 -f ASFV.primers.csv -i FAT94769_pass_barcode02_66883b35_0/polished_clipped_amplicons.fa --threads 8 --no_split -o FAT94769_pass_barcode02_66883b35_0/polished_trimmed.fa (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

tboonf commented 2 years ago

@amandawarr
Upon checking, it seems like the issue could have been due to the unregonizable -f option in porechop

“porechop: error: unrecognized arguments: -format ASFV.primers.csv”

I have followed the porechop installation step as in https://github.com/sclamons/Porechop-1 but it seems like it did not install the updated version which included the -f option used in LILO. Would appreciate suggestion and advice to resolve this