Hello qiime2 users and team,
I am relatively new to this programme and after going through the main tutorials I tried to use qiime2 (2018.8) to import a big FASTA and create a feature table with vsearch dereplicate (since, as far as I know, dada2 and deblur are not an option for a FASTA without quality).
All good importing the file, but when I tried to dereplicate I incurred in this error which I don't know how to interpret: IndexError: list index out of range - I searched for similar error in this forum, but found none. Sorry if it's a duplicate.
Here's the code I used:
> qiime vsearch dereplicate-sequences\
> --i-sequences CoDL-CH0001.qza\
> --o-dereplicated-sequences CoDL-CH0001-derep.qza\
> --o-dereplicated-tab\
> --verbose
And this is the full output:
> Running external command line application. This may print messages to stdout and/or stderr. The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. Command: vsearch --derep_fullength /tmp/qiime2-archive-063t149_/cacfdd7b-9595-431e-9dcf-e800bef4d9d7/data/seqs.fna --outpu`Preformatted text`t /tmp/q2-DNAFASTAFormat-ktw_h99w --relabel_sha1 --relabel_keep --uc /tmp/tmpygkkud8x --qmask none --xsize vsearch v2.7.0_linux_x86_64, 7.7GB RAM, 4 cores https://github.com/torognes/vsearch Reading file /tmp/qiime2-archive-063t149_/cacfdd7b-9595-431e-9dcf-e800bef4d9d7/data/seqs.fna 100% 58586982 nt in 156872 seqs, min 356, max 440, avg 373 Dereplicating 100% Sorting 100% 54354 unique sequences, avg cluster 2.9, median 1, max 15423 Writing output file 100% Writing uc file, first part 100% Writing uc file, second part 100% Traceback (most recent call last): File "/home/giacomo_vitali/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__ results = action(**arguments) File "<decorator-gen-128>", line 2, in dereplicate_sequences File "/home/giacomo_vitali/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable output_types, provenance) File "/home/giacomo_vitali/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_ output_views = self._callable(**view_args) File "/home/giacomo_vitali/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/_cluster_sequences.py", line 134, in dereplicate_sequences table = _parse_uc(out_uc) File "/home/giacomo_vitali/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/_cluster_sequences.py", line 70, in _parse_uc observation_id = fields[9].split()[0] IndexError: list index out of range
Any idea of what may be going on here?
Thank you all,
Giacomo
