pick otus problem
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louisville 1
Apr 9, 2018, 4:33:07 PM4/9/18
to Qiime 1 Forum
Hi Everybody,
I am still using Qiime 1 and I had a problem when Itried to pick otus. I got the following message.
qiime@qiime-190-virtual-box:~$ pick_open_reference_otus.py -i '/home/qiime/FSU_split/seqs.fna' -o FSU_open_reference_otus
Traceback (most recent call last):
File "/usr/local/bin/pick_open_reference_otus.py", line 453, in <module>
main()
File "/usr/local/bin/pick_open_reference_otus.py", line 432, in main
minimum_failure_threshold=minimum_failure_threshold)
File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/pick_open_reference_otus.py", line 713, in pick_subsampled_open_reference_otus
close_logger_on_success=False)
File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:
*** ERROR RAISED DURING STEP: Pick Reference OTUs
Command run was:
pick_otus.py -i /home/qiime/FSU_split/seqs.fna -o FSU_open_reference_otus/step1_otus -r /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta -m uclust_ref --suppress_new_clusters
Command returned exit status: 137
Stdout:
Stderr
Killed
louisville 1
Apr 11, 2018, 3:27:30 PM4/11/18
to Qiime 1 Forum
Hi Everybody,
I sent email about failing pick_otus but I didn't get any reply. I keep getting the same error. These are my own Miseq sequencing in the lab. Please help. Thanks
Bassam
TonyWalters
Apr 11, 2018, 3:34:35 PM4/11/18
to Qiime 1 Forum
That has been a memory issue before (try allocating more to the virtual box if possible). See https://groups.google.com/forum/#!topic/qiime-forum/zYKzu0ljSEg
louisville 1
Apr 11, 2018, 4:21:56 PM4/11/18
to Qiime 1 Forum
I increased the memory and I had this error. Thanks
Bassam
qiime@qiime-190-virtual-box:~$ pick_open_reference_otus.py -i '/home/qiime/FSU_split/seqs.fna' -o FSU_open_otus
Traceback (most recent call last):
File "/usr/local/bin/pick_open_reference_otus.py", line 453, in <module>
main()
File "/usr/local/bin/pick_open_reference_otus.py", line 432, in main
minimum_failure_threshold=minimum_failure_threshold)
File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/pick_open_reference_otus.py", line 713, in pick_subsampled_open_reference_otus
close_logger_on_success=False)
File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:
*** ERROR RAISED DURING STEP: Pick Reference OTUs
Command run was:
pick_otus.py -i /home/qiime/FSU_split/seqs.fna -o FSU_open_otus/step1_otus -r /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta -m uclust_ref --suppress_new_clusters
Command returned exit status: 1
Stdout:
Stderr
Traceback (most recent call last):
File "/usr/local/bin/pick_otus.py", line 1004, in <module>
main()
File "/usr/local/bin/pick_otus.py", line 924, in main
failure_path=failure_path)
File "/usr/local/lib/python2.7/dist-packages/qiime/pick_otus.py", line 1912, in __call__
HALT_EXEC=HALT_EXEC)
File "/usr/local/lib/python2.7/dist-packages/bfillings/uclust.py", line 580, in get_clusters_from_fasta_filepath
HALT_EXEC=HALT_EXEC)
File "/usr/local/lib/python2.7/dist-packages/bfillings/uclust.py", line 481, in uclust_cluster_from_sorted_fasta_filepath
app_result = app({'--input': fasta_filepath, '--uc': output_filepath})
File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 284, in __call__
'StdOut:\n%s\n' % open(outfile).read() +
IOError: [Errno 2] No such file or directory: '/tmp/tmpzdUieiGvgp8KbLRPEqiY.txt
TonyWalters
Apr 12, 2018, 12:53:14 AM4/12/18
to Qiime 1 Forum
Hi, I'm not totally sure how to solve this, but here are some other threads with similar errors you might check:
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