mpileup: invalid option -- 't'

[Mx-Chpl]

Hello, I want to use the last version of ARIBA (XXX) but an error occured when I ran ariba test or directly my samples. Here all the error messages (with ariba test) : _ Assembling each cluster ___ Will run 1 cluster(s) in parallel Not constructing cluster cluster because it only has 2 reads (1 of 9) Constructing cluster cluster_1 (2 of 9) Constructing cluster cluster_2 (3 of 9) Constructing cluster cluster_3 (4 of 9) Constructing cluster cluster_4 (5 of 9) Constructing cluster gene (6 of 9) Constructing cluster gene_1 (7 of 9) Constructing cluster noncoding (8 of 9) Constructing cluster noncoding_1 (9 of 9) Start running cluster cluster_1 in directory /home/chapelm/Ariba_test/OUT/ariba.tmp.1fuiuzdn/cluster_1 cluster_1 detected 1 threads available to it mpileup: invalid option -- 't' Failed cluster: cluster_1 Finished running cluster cluster_1 in directory /home/chapelm/Ariba_test/OUT/ariba.tmp.1fuiuzdn/cluster_1 Deleting cluster dir /home/chapelm/Ariba_test/OUT/ariba.tmp.1fuiuzdn/cluster_1 Other clusters failed. Will not start cluster cluster_2 Other clusters failed. Will not start cluster cluster_3 Other clusters failed. Will not start cluster cluster_4 Other clusters failed. Will not start cluster gene Other clusters failed. Will not start cluster gene_1 Other clusters failed. Will not start cluster noncoding Other clusters failed. Will not start cluster noncoding_1 Final value of remaining_clusters counter: Value('l', 7) Finished assembling clusters

Traceback (most recent call last): File "/Softs/virtualenvPython/Ariba_2.14.6/lib64/python3.6/site-packages/ariba/clusters.py", line 612, in run self._run() File "/Softs/virtualenvPython/Ariba_2.14.6/lib64/python3.6/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 "/Softs/virtualenvPython/Ariba_2.14.6/bin/ariba", line 312, in args.func(args) File "/Softs/virtualenvPython/Ariba_2.14.6/lib64/python3.6/site-packages/ariba/tasks/run.py", line 65, in run c.run() File "/Softs/virtualenvPython/Ariba_2.14.6/lib64/python3.6/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...

Something went wrong. See above for error message(s). Return code was 1

It seems to be an error with mpileup but I am not sure.

[emollier]

This looks to be a duplicate of #327 and can probably be closed now that it is properly addressed. Have a nice day, :) Étienne.

[martinghunt]

Thank you! Yes, is duplicate