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Hi all. Hitting a TIDDIT error I don't understand:...
# sarek
m
Hi all. Hitting a TIDDIT error I don't understand:
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Command error:
  /usr/local/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice.
    return _methods._mean(a, axis=axis, dtype=dtype,
  /usr/local/lib/python3.8/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide
    ret = ret.dtype.type(ret / rcount)
detail in thread if anyone has any ideas
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Command executed:

  tiddit \
      --sv \
      --skip_assembly \
      --threads 6 \
      --bam H37004_UCLA-20240606_20240606_N.recal.cram \
      --ref Homo_sapiens_assembly38.fasta \
      -o H37004_UCLA-20240606_20240606_N.tiddit
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_TIDDIT:TIDDIT_SV":
      tiddit: $(echo $(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  Collecting signals on contig: chr11_KI270903v1_alt
  Collecting signals on contig: chr15_KI270905v1_alt
  Collecting signals on contig: chr17_KI270909v1_alt
  Collecting signals on contig: chr18_KI270912v1_alt
  Collecting signals on contig: chr22_KB663609v1_alt
  Collecting signals on contig: chr19_KI270915v1_alt
  Collecting signals on contig: chr19_KI270919v1_alt
  Collecting signals on contig: chr19_KI270923v1_alt
  Collecting signals on contig: chr6_GL000252v2_alt
  Collecting signals on contig: chr22_KI270928v1_alt
  Collecting signals on contig: chr19_KI270931v1_alt
  Collecting signals on contig: chr3_KI270934v1_alt
  Collecting signals on contig: chr3_KI270935v1_alt
  Collecting signals on contig: chr6_GL000255v2_alt
  Collecting signals on contig: chr6_GL000256v2_alt
  Collecting signals on contig: chr19_GL949753v2_alt
  Collecting signals on contig: chrUn_KN707673v1_decoy
  Collecting signals on contig: chrUn_KN707740v1_decoy
  Collecting signals on contig: chrUn_KN707779v1_decoy
  Collecting signals on contig: chrUn_KN707862v1_decoy
  Collecting signals on contig: chrUn_KN707925v1_decoy
  Collecting signals on contig: chrUn_KN707963v1_decoy
  Collecting signals on contig: chrUn_JTFH01000001v1_decoy
  Collecting signals on contig: chrUn_JTFH01000004v1_decoy
  Collecting signals on contig: chrUn_JTFH01001735v1_decoy
  Collecting signals on contig: HLA-DRB1*01:01:01
  Collecting signals on contig: HLA-DRB1*07:01:01:01
  Collecting signals on contig: HLA-DRB1*10:01:01
  Collecting signals on contig: HLA-DRB1*12:01:01
  Collecting signals on contig: HLA-DRB1*14:05:01
  Collecting signals on contig: HLA-DRB1*15:01:01:02
  Collecting signals on contig: HLA-DRB1*15:03:01:01
  Collecting signals on contig: HLA-DRB1*16:02:01
  Collecting signals on contig: chr5
  Collecting signals on contig: chr7
  Collecting signals on contig: chr15
  Collecting signals on contig: chr21
  Collecting signals on contig: chrY
  Collecting signals on contig: chr2
  Collecting signals on contig: chr11
  Collecting signals on contig: chr17
  Collecting signals on contig: chrX
  total 1831.6027884483337
  Writing signals to file
  extracted signals in:
  -1894.7505276203156
  calculated coverage in:
  132.4579038619995
  generated clusters in
  130.00103425979614

Command error:
  /usr/local/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice.
    return _methods._mean(a, axis=axis, dtype=dtype,
  /usr/local/lib/python3.8/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide
    ret = ret.dtype.type(ret / rcount)
this is on WGS data, 1 normal and 3 tumor samples in the same run - this appears to be the germline sample
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Feb-15 00:50:59.371 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_TIDDIT:TIDDIT_SV (H37004_UCLA-20240606_20240606_N)'
I think this may be a red herring the task appears to have hit the process_medium time limit (8h) curious if folks have any suggestions as to why it's not reporting the time limit issue
t
I'm not sure -- you could rerun it with more time and see if that helps, but maybe it died right at the time limit with a "legitimate" error. 
RuntimeWarning: Mean of empty slice.
could result in 
RuntimeWarning: invalid value encountered in scalar divide
if this is a divide by zero. All of these appear to be warnings, though, not errors that would kill the program, and 
Writing signals to file
sounds like it was in the process of finishing without errors. Does the work directory contain all file the way you would expect them? Either way, I would make sure this is reproducible before speculating too much.
m
yeah, it's definitely a timeout; not sure if the swallowed error was AWS or nextflow
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