Hey,
Here is the complete log:
(qiime2-2019.7) 17192451@qiime2-bestlab:/home/17192451/ghost$ more /tmp/qiime2-q2cli-err-6q9_sf14.log
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 wil
l depend on temporary files that no longer exist.
Command: vsearch --usearch_global /tmp/tmpuczm5u0_ --id 0.85 --db /tmp/qiime2-ar
chive-w4w_0a13/7eb8d9ad-42d8-409f-95ae-162bcc0f7167/data/dna-sequences.fasta --u
c /tmp/tmpspkmnh3p --strand plus --qmask none --notmatched /tmp/tmpcjsll053 --th
reads 1
vsearch v2.7.0_linux_x86_64, 15.6GB RAM, 8 cores
Reading file /tmp/qiime2-archive-w4w_0a13/7eb8d9ad-42d8-409f-95ae-162bcc0f7167/d
ata/dna-sequences.fasta 100%
19748835 nt in 35667 seqs, min 205, max 3526, avg 554
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching
Fatal error: Invalid (zero) abundance annotation in FASTA file header
Traceback (most recent call last):
File “/UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-123>”, line 2, in cluster_features_closed_reference
File “/UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/_cluster_features.py”, line 256, in cluster_features_closed_reference
run_command(cmd)
File "/UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/cluster_features.py", line 33, in run_command
subprocess.run(cmd, check=True)
File “/UBC-O/17192451/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '[‘vsearch’, ‘–usearch_global’, '/tmp/tmpuczm5u0’, ‘–id’, ‘0.85’, ‘–db’, ‘/tmp/qiime2-archive-w4w_0a13/7eb8d9ad-42d8-409f-95ae-162bcc0f7167/data/dna-sequences.fasta’, ’
–uc’, ‘/tmp/tmpspkmnh3p’, ‘–strand’, ‘plus’, ‘–qmask’, ‘none’, ‘–notmatched’, ‘/tmp/tmpcjsll053’, ‘–threads’, ‘1’]’ returned non-zero exit status 1.
I have noticed the fatal error and I have seen that in other posts for different reasons. Which file is this and how can I correct it? Thanks!