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NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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Error executing process > 'FCSGX_RUNGX (hifiasm-decontaminated-default-hap0)' #80

Closed Estel-Kitsune closed 7 months ago

Estel-Kitsune commented 7 months ago

Error

Error executing process > 'FCSGX_RUNGX (hifiasm-decontaminated-default-hap0)'  

Caused by:
  Process `FCSGX_RUNGX (hifiasm-decontaminated-default-hap0)` terminated with an error exit status (140)

Command executed:

  export GX_NUM_CORES=12
  run_gx.py \
      --fasta hifiasm-raw-default.asm.bp.p_ctg.fasta.gz \
      --gx-db gxdb_all \
      --tax-id 57642 \
      --out-basename hifiasm-decontaminated-default-hap0 \
      --out-dir . \

  cat <<-END_VERSIONS > versions.yml
  "FCSGX_RUNGX":
      fcs_gx: 0.5.0
  END_VERSIONS

Command exit status:
  140

Command output:
  (empty)

Command error:
  egrep: warning: egrep is obsolescent; using grep -E
  egrep: warning: egrep is obsolescent; using grep -E
  egrep: warning: egrep is obsolescent; using grep -E
  egrep: warning: egrep is obsolescent; using grep -E
  egrep: warning: egrep is obsolescent; using grep -E
  [...many more...]

Run info N E X T F L O W ~ version 22.10.2 Launching https://github.com/NBISweden/Earth-Biogenome-Project-pilot [awesome_wescoff] DSL2 - revision: 45ea5ddb38 [main]

mahesh-panchal commented 7 months ago

Exit code 140 usually means resources were not enough. Check slurm to see whether it was out of memory, or a time out. My guess is probably a time out.

Estel-Kitsune commented 7 months ago

Content of .command.err

INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO:    Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E

-----------------------------------------------------------------------------

tax-id    : 57642
fasta     : hifiasm-raw-default.asm.bp.p_ctg.fasta.gz
size      : 252.6 MiB
split-fa  : True
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
BLAST-div : gastropods
gx-div    : anml:molluscs
w/same-tax: True
bin-dir   : /usr/local/bin
gx-db     : gxdb_all/all.gxi
gx-ver    : Jan  9 2024 20:12:29; git:+branch--
output    : ./hifiasm-decontaminated-default-hap0.taxonomy.rpt

-----------------------------------------------------------------------------

    Warning: The host does not have enough physical memory for the gx-database.
    The execution is likely to be extremely slow due to disk thrashing, and suitable only for tiny genomes (e.g. bacteria).
    Virtual memory paging does not provide adequate performance.
    See https://github.com/ncbi/fcs/wiki/FCS-GX for details.

egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
[...]
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
Collecting masking statistics...
Using GX_NUM_CORES=12
egrep: warning: egrep is obsolescent; using grep -E
[...]
egrep: warning: egrep is obsolescent; using grep -E
Collected masking stats:  0.878724 Gbp; 24.3732s; 36.0528 Mbp/s. Baseline: 1.96825

Using GX_NUM_CORES=12
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
[...]
Estel-Kitsune commented 7 months ago

Yes, time limit: slurmstepd: error: JOB 45039282 ON r189 CANCELLED AT 2024-02-15T10:13:28 DUE TO TIME LIMIT