https://nf-co.re logo
Join Slack
Powered by
[nf-core/funcscan] Pipeline completed with errors-...
# funcscan
a
[nf-core/funcscan] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_FUNCSCANFUNCSCANARG:RGI_MAIN (bc16)' Caused by: Process exceeded running time limit (1h) Command executed: DB_VERSION=$(ls card_database_processed/card_database_*_all.fasta | sed "s/card_database_processed\/card_database_v\([0-9].*[0-9]\).*/\1/") rgi \ load \ \ --card_json card_database_processed/card.json \ --debug --local \ --card_annotation card_database_processed/card_database_v$DB_VERSION.fasta \ --card_annotation_all_models card_database_processed/card_database_v$DB_VERSION\_all.fasta \ rgi \ main \ \ --num_threads 4 \ --output_file bc16 \ --input_sequence bc16.fasta mkdir temp/ for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e $FILE ]] && mv $FILE temp/; done RGI_VERSION=$(rgi main --version) cat <<-END_VERSIONS > versions.yml "NFCORE_FUNCSCANFUNCSCANARG:RGI_MAIN": rgi: $(echo $RGI_VERSION) rgi-database: $(echo $DB_VERSION) END_VERSIONS Command exit status: - Command output: (empty) Command error: "wildcard_annotation_all_models": null, "wildcard_index": null, "wildcard_version": null, "baits_annotation": null, "baits_index": null, "kmer_database": null, "amr_kmers": null, "kmer_size": null, "local_database": true, "debug": true } INFO 2024-09-05 140020,499 : local_db: True, filepath: card_database_processed/card.json, filename: card.json, validate_json: False INFO 2024-09-05 140020,536 : file card.json loaded ok INFO 2024-09-05 140020,781 : local_db: True, filepath: card_database_processed/card_database_v3.3.0.fasta, filename: card_reference.fasta, validate_json: False INFO 2024-09-05 140020,786 : file card_reference.fasta loaded ok INFO 2024-09-05 140020,786 : loaded card annotation file: card_reference.fasta for 'rgi bwt'. INFO 2024-09-05 140020,786 : local_db: True, filepath: card_database_processed/card_database_v3.3.0_all.fasta, filename: card_reference_all.fasta, validate_json: False INFO 2024-09-05 140020,791 : file card_reference_all.fasta loaded ok INFO 2024-09-05 140020,791 : loaded card annotation file: card_reference_all.fasta for 'rgi bwt'. INFO 2024-09-05 140020,792 : { "card_json": { "data_version": "3.3.0", "model_type_used": [ "homolog", "variant", "rRNA", "overexpression", "knockout" ] }, "card_canonical": { "data_version": "3.3.0", "model_type_used": [ "homolog", "variant", "rRNA", "overexpression", "knockout" ] }, "card_variants": { "data_version": "N/A", "model_type_used": [] }, "card_kmers": { "kmer_sizes": [] } } Matplotlib created a temporary cache directory at /tmp/matplotlib-p3a6ljwm because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. sh: line 1: /usr/local/lib/python3.8/site-packages/app/_db/.ncbirc: Permission denied Work dir: /home/as/nextflow/work/cc/0fa3aa85be6d775e49feb01022f406 Tip: you can replicate the issue by changing to the process work dir and entering the command 
bash .command.run
-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details
j
You need to configure your pipeline to allow it to run rgi for longer than one hour - see the'caused by' message at the top
To do so
resourcehelp
s
You likely need to configure the pipeline to your available computational resources to you machine or infrastructure. Please see the following two(!) sections: - https://nf-co.re/docs/usage/getting_started/configuration#tuning-workflow-resources - https://nf-co.re/docs/usage/getting_started/configuration#max-resources of the documentation for more information.
j
Although
Looking at the bottom the no permissions is odd
moreinfo
s
To help we'd love a few more details please: 1. The Nextflow command you used to launch the pipeline 2. Any custom Nextflow config files 3. The full error message 4. The corresponding 
.nextflow.log
file, where you are running the analysis. Remember to use triple backslashes on their own lines for code blocks. Also take a look at https://nf-co.re/usage/troubleshooting for more information on debugging failed pipelines. Thanks!
a
thank you James i'll try. about the time limit i have to change the config file right?
j
Yes
Well, make a custom one
a
the problem is how 😁
j
Try reading the links I sent above, and you'll have your answer
a
okay perfect 🙂
j
;)
a
Hello , i created a custom nf-params.json and seems working except the mmseqs_taxonomy step , see below
j
I didn't get the 'see below'
Nothing seems ot have been psoted
OK inthis case 
mmseqs
died with a segmentation fault, this is more often than not due to running out of memory,
Copy code
Sep-06 17:16:27.486 [TaskFinalizer-6] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:TAXA_CLASS:MMSEQS_TAXONOMY (bc16)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:TAXA_CLASS:MMSEQS_TAXONOMY (bc16)` terminated with an error exit status (1)


Command executed:

  mkdir -p bc16_taxonomy
  
  # Extract files with specified args based suffix | remove suffix | isolate longest common substring of files
  DB_QUERY_PATH_NAME=$(find -L "bc16/" -maxdepth 1 -name "*.dbtype" | sed 's/\.[^.]*$//' | sed -e 'N;s/^\(.*\).*\n\1.*$/\1\n\1/;D' )
  DB_TARGET_PATH_NAME=$(find -L "mmseqs_database/" -maxdepth 1 -name "*.dbtype" | sed 's/\.[^.]*$//' | sed -e 'N;s/^\(.*\).*\n\1.*$/\1\n\1/;D' )
  
  mmseqs \
      taxonomy \
      $DB_QUERY_PATH_NAME \
      $DB_TARGET_PATH_NAME \
      bc16_taxonomy/bc16 \
      tmp1 \
      --remove-tmp-files --search-type 3 --lca-ranks kingdom,phylum,class,order,family,genus,species --tax-lineage 1 -s 5.0 --orf-filter-s 2.0 --lca-mode 3 --vote-mode 1 \
      --threads 12 \
      --compressed 1
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:TAXA_CLASS:MMSEQS_TAXONOMY":
      mmseqs: $(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //')
  END_VERSIONS

Command exit status:
  1

Command output:
  Reverse frames                         	1,2,3
  Translation table                      	1
  Translate orf                          	0
  Use all table starts                   	false
  Offset of numeric ids                  	0
  Create lookup                          	0
  Add orf stop                           	false
  Overlap between sequences              	0
  Sequence split mode                    	1
  Header split mode                      	0
  Chain overlapping alignments           	0
  Merge query                            	1
  Search type                            	3
  Prefilter mode                         	0
  Exhaustive search mode                 	false
  Filter results during exhaustive search	0
  Strand selection                       	1
  LCA search mode                        	false
  Disk space limit                       	0
  MPI runner                             	
  Force restart with latest tmp          	false
  Remove temporary files                 	true
  
  Accel. 2bLCA cannot be used with nucl-nucl taxonomy, using top-hit instead
  Create directory tmp1/16159046800325979006/tmp_hsp1
  search bc16/bc16 mmseqs_database/database tmp1/16159046800325979006/first tmp1/16159046800325979006/tmp_hsp1 --alignment-mode 1 -e 1 --max-rejected 5 --max-accept 30 --threads 12 --compressed 1 -s 5 --spaced-kmer-mode 1 --min-length 30 --max-length 32734 --orf-start-mode 1 --search-type 3 --remove-tmp-files 1 
  
  splitsequence mmseqs_database/database tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/target_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --create-lookup 0 --threads 12 --compressed 1 -v 3 
  
  Sequence split mode (--sequence-split-mode 0) and compressed (--compressed 1) can not be combined.
  Turn compressed to 0[=================================================================] 225 0s 7ms
  Time for merging to target_seqs_split_h: 0h 0m 0s 12ms
  Time for merging to target_seqs_split: 0h 0m 0s 12ms
  Time for processing: 0h 0m 0s 51ms
  extractframes bc16/bc16 tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/query_seqs --forward-frames 1 --reverse-frames 1 --create-lookup 0 --threads 12 --compressed 1 -v 3 
  
  [=================================================================] 417.86K 3s 115ms
  Time for merging to query_seqs_h: 0h 0m 0s 187ms
  Time for merging to query_seqs: 0h 0m 1s 107ms
  Time for processing: 0h 0m 5s 107ms
  splitsequence tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/query_seqs tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/query_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --create-lookup 0 --threads 12 --compressed 1 -v 3 
  
  Sequence split mode (--sequence-split-mode 0) and compressed (--compressed 1) can not be combined.
  Turn compressed to 0=[================================================================] 835.72K 0s 101ms
  Time for merging to query_seqs_split_h: 0h 0m 0s 160ms
  Time for merging to query_seqs_split: 0h 0m 0s 187ms
  Time for processing: 0h 0m 0s 795ms
  Error: Prefilter died
  Error: Search step died
  Error: First search died

Command error:
  Translation table                      	1
  Translate orf                          	0
  Use all table starts                   	false
  Offset of numeric ids                  	0
  Create lookup                          	0
  Add orf stop                           	false
  Overlap between sequences              	0
  Sequence split mode                    	1
  Header split mode                      	0
  Chain overlapping alignments           	0
  Merge query                            	1
  Search type                            	3
  Prefilter mode                         	0
  Exhaustive search mode                 	false
  Filter results during exhaustive search	0
  Strand selection                       	1
  LCA search mode                        	false
  Disk space limit                       	0
  MPI runner                             	
  Force restart with latest tmp          	false
  Remove temporary files                 	true
  
  Accel. 2bLCA cannot be used with nucl-nucl taxonomy, using top-hit instead
  Create directory tmp1/16159046800325979006/tmp_hsp1
  search bc16/bc16 mmseqs_database/database tmp1/16159046800325979006/first tmp1/16159046800325979006/tmp_hsp1 --alignment-mode 1 -e 1 --max-rejected 5 --max-accept 30 --threads 12 --compressed 1 -s 5 --spaced-kmer-mode 1 --min-length 30 --max-length 32734 --orf-start-mode 1 --search-type 3 --remove-tmp-files 1 
  
  splitsequence mmseqs_database/database tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/target_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --create-lookup 0 --threads 12 --compressed 1 -v 3 
  
  Sequence split mode (--sequence-split-mode 0) and compressed (--compressed 1) can not be combined.
  Turn compressed to 0[=================================================================] 225 0s 7ms
  Time for merging to target_seqs_split_h: 0h 0m 0s 12ms
  Time for merging to target_seqs_split: 0h 0m 0s 12ms
  Time for processing: 0h 0m 0s 51ms
  extractframes bc16/bc16 tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/query_seqs --forward-frames 1 --reverse-frames 1 --create-lookup 0 --threads 12 --compressed 1 -v 3 
  
  [=================================================================] 417.86K 3s 115ms
  Time for merging to query_seqs_h: 0h 0m 0s 187ms
  Time for merging to query_seqs: 0h 0m 1s 107ms
  Time for processing: 0h 0m 5s 107ms
  splitsequence tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/query_seqs tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/query_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --create-lookup 0 --threads 12 --compressed 1 -v 3 
  
  Sequence split mode (--sequence-split-mode 0) and compressed (--compressed 1) can not be combined.
  Turn compressed to 0=[================================================================] 835.72K 0s 101ms
  Time for merging to query_seqs_split_h: 0h 0m 0s 160ms
  Time for merging to query_seqs_split: 0h 0m 0s 187ms
  Time for processing: 0h 0m 0s 795ms
  tmp1/16159046800325979006/tmp_hsp1/17210119921787064669/blastp.sh: line 135:   665 Segmentation fault      (core dumped) $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMP_PATH/pref_$STEP" $PREFILTER_PAR -s "$SENS"
  Error: Prefilter died
  Error: Search step died
  Error: First search died

Work dir:
  /home/as/nextflow/work/bf/da2dcddbb86138e408958be36cdef9
You should try increasing the memory using for the 
MMSEQS_TAXONOMY
process again as with the links above 🙂
8 Views
Open in Slack
PreviousNext
Powered by