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biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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Error while removing intermediate files after running biobakery 16s pipeline #20

Closed evilvenom closed 2 years ago

evilvenom commented 2 years ago

Error log:

[Errno 1] Command `remove_if_exists.py /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2 --is-folder ; picrust2_pipeline.py -s /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/all_samples_closed_reference_picrust_reformatted_input.fasta -i /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/all_samples_taxonomy_closed_reference_picrust_reformatted_input.tsv -o /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2 -p 8 ' failed. 
  Out: b''
  Err: b'\nError running this command:\nplace_seqs.py --study_fasta /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/all_samples_closed_reference_picrust_reformatted_input.fasta --ref_dir /home/tgb2/picrust2/picrust2/default_files/prokaryotic/pro_ref --out_tree /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/out.tre --processes 8 --intermediate /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng\n\nStandard error of the above failed command:\n\nError running this command:\nepa-ng --tree /home/tgb2/picrust2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 8 -m /home/tgb2/picrust2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100\n\nStandard output of the above failed command:\nINFO Selected: Output dir: /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/epa_out/\nINFO Selected: Query file: /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/study_seqs_hmmalign.fasta\nINFO Selected: Tree file: /home/tgb2/picrust2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre\nINFO Selected: Reference MSA: /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/ref_seqs_hmmalign.fasta\nINFO Selected: Filtering by accumulated threshold: 0.99\nINFO Selected: Maximum number of placements per query: 100\nINFO Selected: Automatic switching of use of per rate scalers\nINFO Selected: Preserving the root of the input tree\nINFO Selected: Specified model file: /home/tgb2/picrust2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model\nINFO Selected: Reading queries in chunks of: 5000\nINFO Selected: Using threads: 8\nINFO     ______ ____   ___           _   __ ______\n        / ____// __ \\ /   |         / | / // ____/\n       / __/  / /_/ // /| | ______ /  |/ // / __  \n      / /___ / ____// ___ |/_____// /|  // /_/ /  \n     /_____//_/    /_/  |_|      /_/ |_/ \\____/ (v0.3.8)\nINFO Using model parameters:\nINFO    Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 0.453141 (user),  weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177) \n        Base frequencies (user): 0.229585 0.22008 0.298596 0.251739 \n        Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1\nINFO Output file: /mnt/D4C4F524C4F5098E/Tanay/tanay/16s_stool_sample/output1/picrust2/intermediate/place_seqs/epa_out/epa_result.jplace\n\n\n'

Traceback (most recent call last):
  File "/home/tgb2/anaconda3/envs/biobakery/bin/16s.py", line 184, in <module>
    workflow.go()
  File "/home/tgb2/anaconda3/envs/biobakery/lib/python3.6/site-packages/anadama2/workflow.py", line 801, in go
    self._handle_finished()
  File "/home/tgb2/anaconda3/envs/biobakery/lib/python3.6/site-packages/anadama2/workflow.py", line 833, in _handle_finished
    raise RunFailed()
anadama2.workflow.RunFailed

If you could help me with a possible fix, it would be really helpful!

github-actions[bot] commented 2 years ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.