Error when executing pipeline on AWS with fusion mounts

[kojix2]

Hi, this is kojix2.

I'm a newbie and have very little understanding of what bcellmagic is a workflow for. First, to understand what bcellmagic can do, I ran -profile test,docker in Nextflow Tower and got the following error.

What are the possible causes of this?

 Workflow execution completed unsuccessfully

The exit status of the task that caused the workflow execution to fail was: 1

Error executing process > 'NFCORE_BCELLMAGIC:BCELLMAGIC:ALAKAZAM_SHAZAM_REPERTOIRES (report)'

Caused by:
  Essential container in task exited

Command executed:

  execute_report.R repertoire_comparison.Rmd
  Rscript -e "library(alakazam); write(x=as.character(packageVersion('alakazam')), file='alakazam.version.txt')"
  Rscript -e "library(shazam); write(x=as.character(packageVersion('shazam')), file='shazam.version.txt')"
  echo $(R --version 2>&1) | awk -F' '  '{print $3}' > R.version.txt

Command exit status:
  1

Command output:
    |............................................................          |  86%
    ordinary text without R code

    |                                                                            
    |..............................................................        |  88%
  label: unnamed-chunk-10 (with options) 
  List of 4
   $ echo     : logi FALSE
   $ fig.width: num 10
   $ fig.asp  : num 0.8
   $ fig.align: chr "center"

    |                                                                            
    |...............................................................       |  91%
    ordinary text without R code

    |                                                                            
    |.................................................................     |  93%
  label: unnamed-chunk-11 (with options) 
  List of 4
   $ echo     : logi FALSE
   $ fig.width: num 10
   $ fig.asp  : num 0.8
   $ fig.align: chr "center"

    |                                                                            
    |...................................................................   |  95%
    ordinary text without R code

    |                                                                            
    |....................................................................  |  98%
  label: unnamed-chunk-12 (with options) 
  List of 4
   $ echo     : logi FALSE
   $ fig.width: num 10
   $ fig.asp  : num 0.8
   $ fig.align: chr "center"

    |                                                                            
    |......................................................................| 100%
    ordinary text without R code

  /usr/local/bin/pandoc +RTS -K512m -RTS repertoire_comparison.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/nxf.XXXXj9Glzr/Bcellmagic_report.html --lua-filter /usr/local/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/library/rmarkdown/rmd/h/default.html --highlight-style pygments --variable theme=bootstrap --css nf-core_style.css --include-in-header /tmp/Rtmp9ZwV8C/rmarkdown-str3a595dbe04.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --citeproc 

Command error:

  processing file: repertoire_comparison.Rmd
  output file: repertoire_comparison.knit.md

  File ./references.bibtex not found in resource path
  Error: pandoc document conversion failed with error 99
  Execution halted

Work dir:
  /fusion/s3/ABCDEFG/bcellmagic/wd/25/96cdb23bc7f02ad73b2a5a2e087162

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

[kojix2]

[ggabernet]

This has been fixed in #164 and will be added to the next release.