ariba.clusters.Error: At least one cluster failed

[JFsanchezherrero]

Hi there,

I keep on obtaining an error when running ARIBA and VFDB information. From 96 samples, ARIBA failed in 2 samples given the same log details:

Error making report for cluster sdrC_1 ... traceback:
Traceback (most recent call last):
File "/path/to_env/lib/python3.8/site-packages/ariba/cluster.py", line 462, in _run
self.report_lines = report.report_lines(self)
File "/path/to_env/lib/python3.8/site-packages/ariba/report.py", line 375, in report_lines
lines.extend(_report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, contig_pymummer_variants))
File "/path/to_env/python3.8/site-packages/ariba/report.py", line 332, in _report_lines_for_one_contig
ref_nt = cluster.ref_sequence[ref_coord]
File "/path/to_env/python3.8/site-packages/pyfastaq/sequences.py", line 423, in getitem
return self.seq[index]
IndexError: string index out of range
Failed cluster: sdrC_1
Other clusters failed. Will not start cluster sdrD
Other clusters failed. Will not start cluster sdrE
...
Other clusters failed. Will not start cluster vWbp
Other clusters failed. Will not start cluster sasC
Other clusters failed. Will not start cluster sasG
Traceback (most recent call last):
File "/path/to_env/lib/python3.8/site-packages/ariba/clusters.py", line 612, in run
self._run()
File "/path/to_env/lib/python3.8/site-packages/ariba/clusters.py", line 646, in _run
raise Error('At least one cluster failed! Stopping...')
ariba.clusters.Error: At least one cluster failed! Stopping...

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/path/to_env/bin/ariba", line 312, in
args.func(args)
File "/path/to_env/lib/python3.8/site-packages/ariba/tasks/run.py", line 65, in run
c.run()
File "/path/to_env/lib/python3.8/site-packages/ariba/clusters.py", line 615, in run
raise Error('Something went wrong during ariba run. Cannot continue. Error was:\n' + str(err))
ariba.clusters.Error: Something went wrong during ariba run. Cannot continue. Error was:
At least one cluster failed! Stopping...

I guess the error might be in the retrieval of coordinates from the reference fasta. (string index out of range)

Using the same exact database It succeeded to finish for the remaining samples and same gene sdrC_1 was successfully identified or missing accordingly. Also, using a different database, CARD, both samples were correctly analyzed and successfully finished.

Version details:

ARIBA version: 2.14.6

External dependencies:
bowtie2 2.4.1 /soft/bin/bowtie2
cdhit 4.6 /software/debian-8/bio/cdhit-4.6.4/cd-hit-est
nucmer 4.0.0beta2 /soft/bin/nucmer
spades ERROR /soft/bin/spades.py

External dependencies OK: True

Python version:
3.8.2 (default, Mar 20 2020, 17:35:03)
[GCC 8.3.0]

Python packages:
ariba 2.14.6 /path/to_env/lib/python3.8/site-packages/ariba/init.py
bs4 4.9.1 /path/to_env/lib/python3.8/site-packages/bs4/init.py
dendropy 4.4.0 /path/to_env/lib/python3.8/site-packages/dendropy/init.py
pyfastaq 3.17.0 /path/to_env/lib/python3.8/site-packages/pyfastaq/init.py
pymummer 0.10.3 /path/to_env/lib/python3.8/site-packages/pymummer/init.py
pysam 0.16.0.1 /path/to_env/lib/python3.8/site-packages/pysam/init.py

** Note: I modified absolute path for clarification purposes.