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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
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process `MEGAN_RMA2INFO` JavaFX detected no fonts error #385

Closed MajoroMask closed 11 months ago

MajoroMask commented 11 months ago

Description of the bug

I already report this under nf-core/modules (this one: https://github.com/nf-core/modules/issues/3887). Since I find it while using taxprofiler, I think I should also post it here.

Command used and terminal output

nextflow run nf-core/taxprofiler -profile test,docker --outdir test --run_malt

Relevant files

[22/c8fab0] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2612.merged)
[6c/c7dab0] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|ERX5474930_ERR5766174_1)
[c7/f3d93a] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|ERR3201952.merged)
[6c/c7dab0] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|ERX5474930_ERR5766174_1)` terminated with an error exit status (137) -- Execution is retried (1)
[22/c8fab0] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2612.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[99/23fcb6] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|2613_ERR5766181.unmapped)
[c7/f3d93a] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|ERR3201952.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[2b/8ec7ee] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|2612.merged)
[99/23fcb6] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|2613_ERR5766181.unmapped)` terminated with an error exit status (137) -- Execution is retried (1)
[02/ed4ceb] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|ERR3201952.merged)
[02/ed4ceb] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|ERR3201952.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[81/7be8b7] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|ERR3201952.merged)
[2b/8ec7ee] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|2612.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[61/03b009] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|2612.merged)
[61/03b009] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|2612.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[69/5f67e9] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|2613_ERR5766181.unmapped)
[81/7be8b7] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|ERR3201952.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[4a/a40995] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|ERX5474930_ERR5766174_1)
[4a/a40995] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|ERX5474930_ERR5766174_1)` terminated with an error exit status (137) -- Execution is retried (1)
[76/98cedd] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|ERX5474930_ERR5766174_1)
[69/5f67e9] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|2613_ERR5766181.unmapped)` terminated with an error exit status (137) -- Execution is retried (1)
[ad/5f4ffc] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|ERX5474930_ERR5766174_1)
[76/98cedd] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|ERX5474930_ERR5766174_1)` terminated with an error exit status (137) -- Execution is retried (1)
[2d/15d14a] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2613_ERR5766181.unmapped)
[ad/5f4ffc] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|ERX5474930_ERR5766174_1)` terminated with an error exit status (137) -- Execution is retried (1)
[12/34ea0a] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|ERR3201952.merged)
[2d/15d14a] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2613_ERR5766181.unmapped)` terminated with an error exit status (137) -- Execution is retried (1)
[aa/7f4a83] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|2612.merged)
[12/34ea0a] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt95|ERR3201952.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[08/7bd852] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|2613_ERR5766181.unmapped)
[aa/7f4a83] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|2612.merged)` terminated with an error exit status (137) -- Execution is retried (1)
[fe/4090bd] Re-submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2612.merged)
[08/7bd852] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|2613_ERR5766181.unmapped)` terminated with an error exit status (137) -- Execution is retried (1)
[8c/f196d0] Re-submitted process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO_TSV (malt85|ERX5474930_ERR5766174_1)
[15/0a139b] Re-submitted process > NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt85|2613_ERR5766181.unmapped)
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2612.merged)'

Caused by:
  Process `NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA (malt95|2612.merged)` terminated with an error exit status (137)

Command executed:

  rma2info \
      -i 2612.merged.rma6 \
      -o 2612.merged_malt95.txt.gz \
       \
      --read2class Taxonomy

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO_KRONA":
      megan: $(echo $(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
  END_VERSIONS

Command exit status:
  137

Command output:
  (empty)

Command error:
  Error: JavaFX detected no fonts! Please refer to release notes for proper font configuration
  Version   MEGAN Community Edition (version 6.21.7, built 23 Jun 2021)
  Author(s) Daniel H. Huson
  Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
  Loading ncbi.map: 2,302,807
  Loading ncbi.tre: /usr/local/bin/rma2info: line 39:    36 Killed                  $java $java_flags --module-path=$modulepath --add-modules=megan megan.tools.RMA2Info $options

System information

$ nextflow -v
nextflow version 23.04.3.5875

$ uname -a
Linux localhost.localdomain 3.10.0-957.el7.x86_64 #1 SMP Thu Nov 8 23:39:32 UTC 2018 x86_64 GNU/Linux

$ cat /etc/centos-release
CentOS Linux release 7.6.1810 (Core)

$ docker -v
Docker version 20.10.21, build baeda1f
jfy133 commented 11 months ago

In this case the Error: line is a read herring, the tool continues to load anyway.

Exit 137 is an out of memory error, meaning you will need to increase the amount of memory the tool is given via config.

however I'll investigate the issue on modules...!