Error code:
[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
Please look at the error code, I am unable to find what exactly is wrong with the pipeline that it is not ending successfully although I am able to get results, I believe only the last step which involves deletion of intermediate files is failing.