qiime vsearch dereplicate-sequences error "list index out of range"

I am using conda install of Qiime2-2019.4 on a Ubuntu 18.04 machine with 192GB of RAM. I have a FASTA file that is in Qiime1 seqs.fna format. I can import the seqs.fna file as sampledata with no problems. When I try to dereplicate the data vsearch returns a “list index out of range” error. My sample ids do not contain special characters.

##Here is the output:

Command: vsearch --derep_fulllength /tmp/qiime2-archive-y50m_wa7/09772ffd-65f4-47d5-9a34-1e70bf14a5d1/data/seqs.fna --output /tmp/q2-DNAFASTAFormat-tsoz1jrs --relabel_sha1 --relabel_keep --uc /tmp/tmp7to827ce --qmask none --xsize

vsearch v2.7.0_linux_x86_64, 188.9GB RAM, 16 cores

Reading file /tmp/qiime2-archive-y50m_wa7/09772ffd-65f4-47d5-9a34-1e70bf14a5d1/data/seqs.fna 100%
164484216 nt in 360711 seqs, min 456, max 456, avg 456
Dereplicating 100%
Sorting 100%
8703 unique sequences, avg cluster 41.4, median 4, max 26087
Writing output file 100%
Writing uc file, first part 100%
Writing uc file, second part 100%
Traceback (most recent call last):
File “/home/casey/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”,
line 311, in call
results = action(**arguments)
File “</home/casey/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-129>”,
line 2, in dereplicate_sequences
File “/home/casey/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”,
line 231, in bound_callable output_types, provenance)
File “/home/casey/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”,
line 365, in _callable_executor_output_views = self._callable(**view_args)
File “/home/casey/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_vsearch/_cluster_sequences.py”,
line 134, in dereplicate_sequences
table = _parse_uc(out_uc)
File “/home/casey/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_vsearch/_cluster_sequences.py”,
line 70, in _parse_uc
observation_id = fields[9].split()[0]
IndexError: list index out of range

Plugin error from vsearch:

list index out of range
##End of output

How can I resolve this error?

1 Like

I found the problem. It was Windows style end of line characters. I feel foolish for not seeing it earlier.