pick_open_reference_otus.py

[kiddy]

 

Hi

I ran this script and all the input file were within the folder, i got the error, written below. i then ran the same script printing the work directory and I still get the same error.

pick_open_reference_otus.py -i $PWD/16S_HS,S,MR,R_chimeras_filtered.fna -r $PWD/gg.nr.fasta -o $PWD/picked_otus

Error in pick_open_reference_otus.py: No filepaths match pattern/name '/scratch/sysusers/kedibone/RAW_READS/S/16S_HS'. All patterns must be matched at least once.

Please help

[Colin Brislawn]

Good afternoon,

Thanks for posting your full script. I noticed this section:-i $PWD/16S_HS,S,MR,R_chimeras_filtered.fna

I see commas (,) inside of your file name. Qiime uses commas to separate different inputs, so having commas inside your file name confuses qiime.

If you rename your file from -i 16S_HS,S,MR,R_chimeras_filtered.fna to -i $PWD/16S_HS_S_MR_R_chimeras_filtered.fna, this should work better.

Let me know if this works for you,

Colin

[kiddy]

Hi Collin

Thanks, the script is now running

Kiddy