VictorPizarroR
commented
2 months ago Hello! @marcellobeltrami how have solved it? I've this same error now.
Open marcellobeltrami opened 1 year ago
VictorPizarroR
commented
2 months ago Hello! @marcellobeltrami how have solved it? I've this same error now.
marcellobeltrami
commented
2 months ago Hello Victor. It has been a while, but I went back and managed to get it to work. Reading around it seems to be an issues with dependencies being out of date. Your best option is to use the docker image provided here:
For instructions on how to run the docker image look at the ariba repo as they provide a general good guide.
I am happy to provide further help if you are not unfamiliar with docker.
Error when running 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/marcello/Test_data/ariba/test_2/OUT/ariba.tmp.9516apn8/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/marcello/Test_data/ariba/test_2/OUT/ariba.tmp.9516apn8/cluster_1 Deleting cluster dir /home/marcello/Test_data/ariba/test_2/OUT/ariba.tmp.9516apn8/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 "/usr/local/lib/python3.10/dist-packages/ariba/clusters.py", line 612, in run self._run() File "/usr/local/lib/python3.10/dist-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 "/usr/local/bin/ariba", line 312, in
args.func(args)
File "/usr/local/lib/python3.10/dist-packages/ariba/tasks/run.py", line 65, in run
c.run()
File "/usr/local/lib/python3.10/dist-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