Error 14: Bad Address

[idolawoye]

Hi Dan.

I ran into the error message below:

executor` >  local (99)
[d7/15dcfc] process > hash_files (2012-045 / fastq-input)                [100%] 36 of 36 ✔
[67/5d9aa5] process > fastp (2012-045)                                   [100%] 36 of 36 ✔
[e4/85ee02] process > kma_align (2012-227)                               [ 20%] 7 of 35, failed: 1
[97/6552eb] process > kma_result_to_mlst (2012-551)                      [100%] 6 of 6
[0c/024671] process > count_called_alleles (2012-551)                    [100%] 5 of 5
[61/85f527] process > pipeline_provenance (BCCDC-PHL/kma-cgmlst / 0.2.0) [100%] 1 of 1 ✔
[2a/6e9542] process > collect_provenance (2012-551)                      [100%] 6 of 6
ERROR ~ Error executing process > 'kma_align (2011-465)'

Caused by:
  Process `kma_align (2011-465)` terminated with an error exit status (14)

Command executed:

  printf -- "- process_name: kma_align\n"       >> 2011-465_kma_align_provenance.yml
  printf -- "  tools:\n"                        >> 2011-465_kma_align_provenance.yml
  printf -- "    - tool_name: kma\n"            >> 2011-465_kma_align_provenance.yml
  printf -- "      tool_version: $(kma -v 2>&1 | cut -d '-' -f 2)\n" >> 2011-465_kma_align_provenance.yml
  printf -- "      parameters:\n"               >> 2011-465_kma_align_provenance.yml
  printf -- "        - parameter: -ef\n"        >> 2011-465_kma_align_provenance.yml
  printf -- "          value: null\n"           >> 2011-465_kma_align_provenance.yml
  printf -- "        - parameter: -cge\n"       >> 2011-465_kma_align_provenance.yml
  printf -- "          value: null\n"           >> 2011-465_kma_align_provenance.yml
  printf -- "        - parameter: -boot\n"      >> 2011-465_kma_align_provenance.yml
  printf -- "          value: null\n"           >> 2011-465_kma_align_provenance.yml
  printf -- "        - parameter: -1t1\n"       >> 2011-465_kma_align_provenance.yml
  printf -- "          value: null\n"           >> 2011-465_kma_align_provenance.yml
  printf -- "        - parameter: -mem_mode\n"  >> 2011-465_kma_align_provenance.yml
  printf -- "          value: null\n"           >> 2011-465_kma_align_provenance.yml
  printf -- "        - parameter: -and\n"       >> 2011-465_kma_align_provenance.yml
  printf -- "          value: null\n"           >> 2011-465_kma_align_provenance.yml
  
  ln -s /Users/idolawoye/Downloads/bioinfo/Mycobacteria_cgmlst/scheme/Mycobacteria.comp.b .
  ln -s /Users/idolawoye/Downloads/bioinfo/Mycobacteria_cgmlst/scheme/Mycobacteria.length.b .
  ln -s /Users/idolawoye/Downloads/bioinfo/Mycobacteria_cgmlst/scheme/Mycobacteria.name .
  ln -s /Users/idolawoye/Downloads/bioinfo/Mycobacteria_cgmlst/scheme/Mycobacteria.seq.b .
  
  kma       -t 8       -ef       -cge       -boot       -1t1       -mem_mode       -and       -o 2011-465.kma       -t_db /Users/idolawoye/Downloads/bioinfo/Mycobacteria_cgmlst/scheme/Mycobacteria       -ipe 2011-465_R1.trim.fastq.gz 2011-465_R2.trim.fastq.gz       -tmp ../
  
  head -n 1 2011-465.kma.res | tr -d '#' | awk '{print tolower($0)}' | tr $'\t' ',' > 2011-465_kma.csv
  tail -qn+2 2011-465.kma.res | tr -d ' ' | tr $'\t' ',' >> 2011-465_kma.csv
  
  mv 2011-465.kma.mapstat 2011-465_kma_mapstat.tsv

Command exit status:
  14

Command output:
  (empty)

Command error:
  # Collecting k-mer scores.
  # Reading inputfile:	2011-465_R1.trim.fastq.gz 2011-465_R2.trim.fastq.gz
  # Phred scale:	33
  #
  # Total time used for DB loading: 0.04 s.
  #
  # Finding k-mer ankers
  Error: 14 (Bad address)

Work dir:
  /Users/idolawoye/Downloads/work/50/69db0e3f80dd1ce5c85a50facd003c

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

However, when I ran this set of samples on a different PC, they worked just fine. Do you have any ideas why this is failing, seeing as some samples already passed the kma_align step here