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Process pipeline:run_gffcompare (1) terminated with an error exit status (1) #130

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mujeebqadiri6308 opened this issue Nov 26, 2024 · 5 comments
Open

Process pipeline:run_gffcompare (1) terminated with an error exit status (1) #130

mujeebqadiri6308 opened this issue Nov 26, 2024 · 5 comments

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@mujeebqadiri6308
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Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.5.0

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.2.1

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

After a successful run of sample 1, I received the following error when processing one of my samples:

ERROR ~ Error executing process > 'pipeline:run_gffcompare (1)'
Caused by:
  Process `pipeline:run_gffcompare (1)` terminated with an error exit status (1)

Relevant log output

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-transcriptomes for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-transcriptomes v1.5.0.
--------------------------------------------------------------------------------
Searching input for [.bam, .ubam] files.
Doing reference based transcript analysis
[58/77ce95] Submitted process > pipeline:preprocess_ref_annotation
[64/fd835e] Submitted process > checkBamHeaders (1)
[35/042448] Submitted process > pipeline:getVersions
[3c/9c7f9b] Submitted process > pipeline:getParams
[f1/d9ab34] Submitted process > fastcat (1)
[18/6e9bd4] Submitted process > pipeline:build_minimap_index (1)
[36/fdfdc1] Submitted process > pipeline:collectFastqIngressResultsInDir (1)
[32/505266] Submitted process > pipeline:preprocess_reads (1)
[0f/694ec7] Submitted process > pipeline:reference_assembly:map_reads (1)
[18/b49bc6] Submitted process > pipeline:split_bam (1)
[10/085fa9] Submitted process > pipeline:assemble_transcripts (4)
[70/155782] Submitted process > pipeline:assemble_transcripts (11)
[54/6b99a0] Submitted process > pipeline:assemble_transcripts (1)
[b9/01ccdf] Submitted process > pipeline:assemble_transcripts (12)
[36/4eacc3] Submitted process > pipeline:assemble_transcripts (8)
[b0/a94af9] Submitted process > pipeline:assemble_transcripts (7)
[ac/1d9d1f] Submitted process > pipeline:assemble_transcripts (6)
[6d/90f47f] Submitted process > pipeline:assemble_transcripts (9)
[50/2490ed] Submitted process > pipeline:assemble_transcripts (3)
[73/6eae4c] Submitted process > pipeline:assemble_transcripts (10)
[09/5af09d] Submitted process > pipeline:assemble_transcripts (5)
[fa/0b8994] Submitted process > pipeline:assemble_transcripts (2)
[89/f72611] Submitted process > pipeline:assemble_transcripts (13)
[92/afd89a] Submitted process > pipeline:assemble_transcripts (15)
[e5/8e3e22] Submitted process > pipeline:assemble_transcripts (23)
[a1/3e9f3b] Submitted process > pipeline:assemble_transcripts (14)
[35/452640] Submitted process > pipeline:assemble_transcripts (17)
[f7/b827ae] Submitted process > pipeline:assemble_transcripts (16)
[35/6d3e18] Submitted process > pipeline:assemble_transcripts (28)
[d5/75b6ae] Submitted process > pipeline:assemble_transcripts (18)
[28/35299b] Submitted process > pipeline:assemble_transcripts (19)
[b7/9aa1e3] Submitted process > pipeline:assemble_transcripts (20)
[60/52fe41] Submitted process > pipeline:assemble_transcripts (21)
[9e/f06083] Submitted process > pipeline:assemble_transcripts (22)
[c3/9a08b1] Submitted process > pipeline:assemble_transcripts (24)
[d3/a63954] Submitted process > pipeline:assemble_transcripts (25)
[04/fcfd5e] Submitted process > pipeline:assemble_transcripts (26)
[f8/10cb59] Submitted process > pipeline:assemble_transcripts (27)
[93/218e37] Submitted process > pipeline:assemble_transcripts (34)
[42/2b75a9] Submitted process > pipeline:assemble_transcripts (29)
[f8/eb9128] Submitted process > pipeline:assemble_transcripts (30)
[1f/641100] Submitted process > pipeline:assemble_transcripts (31)
[b5/fad5ff] Submitted process > pipeline:assemble_transcripts (32)
[0b/cf406e] Submitted process > pipeline:assemble_transcripts (33)
[a5/30133d] Submitted process > pipeline:assemble_transcripts (36)
[b8/c3883d] Submitted process > pipeline:assemble_transcripts (35)
[20/0da609] Submitted process > pipeline:assemble_transcripts (37)
[4c/69e192] Submitted process > pipeline:assemble_transcripts (45)
[06/d4377a] Submitted process > pipeline:assemble_transcripts (38)
[ef/556e20] Submitted process > pipeline:assemble_transcripts (40)
[a2/87cb32] Submitted process > pipeline:assemble_transcripts (39)
[4a/2b6c73] Submitted process > pipeline:assemble_transcripts (41)
[4c/6069cd] Submitted process > pipeline:assemble_transcripts (43)
[3b/0fa3d4] Submitted process > pipeline:assemble_transcripts (42)
[27/322bf1] Submitted process > pipeline:assemble_transcripts (44)
[60/886d58] Submitted process > pipeline:assemble_transcripts (46)
[0a/bca78c] Submitted process > pipeline:assemble_transcripts (47)
[5d/6a6e53] Submitted process > pipeline:assemble_transcripts (48)
[2b/cab34d] Submitted process > pipeline:assemble_transcripts (51)
[68/b95965] Submitted process > pipeline:assemble_transcripts (52)
[6f/741217] Submitted process > pipeline:assemble_transcripts (49)
[6f/73eae4] Submitted process > pipeline:assemble_transcripts (50)
[ed/6db12b] Submitted process > pipeline:assemble_transcripts (53)
[2a/a793ca] Submitted process > pipeline:assemble_transcripts (55)
[8b/a9319a] Submitted process > pipeline:assemble_transcripts (54)
[b2/d0f228] Submitted process > pipeline:assemble_transcripts (61)
[72/b48213] Submitted process > pipeline:assemble_transcripts (56)
[b0/f9ffb3] Submitted process > pipeline:assemble_transcripts (57)
[b6/1932e6] Submitted process > pipeline:assemble_transcripts (58)
[22/6e75a0] Submitted process > pipeline:assemble_transcripts (59)
[10/e4970e] Submitted process > pipeline:assemble_transcripts (62)
[e3/467498] Submitted process > pipeline:assemble_transcripts (63)
[2e/5eedff] Submitted process > pipeline:assemble_transcripts (60)
[8d/462aeb] Submitted process > pipeline:assemble_transcripts (70)
[34/fffd74] Submitted process > pipeline:assemble_transcripts (64)
[43/b72260] Submitted process > pipeline:assemble_transcripts (68)
[5c/c5b438] Submitted process > pipeline:assemble_transcripts (65)
[d8/5ac0e5] Submitted process > pipeline:assemble_transcripts (66)
[7c/ab0045] Submitted process > pipeline:assemble_transcripts (67)
[9d/fc5656] Submitted process > pipeline:assemble_transcripts (69)
[6d/3b62ae] Submitted process > pipeline:assemble_transcripts (71)
[a1/6dc071] Submitted process > pipeline:assemble_transcripts (72)
[b1/7ef736] Submitted process > pipeline:assemble_transcripts (73)
[ba/2620d2] Submitted process > pipeline:assemble_transcripts (74)
[38/03d193] Submitted process > pipeline:assemble_transcripts (75)
[f2/3970dd] Submitted process > pipeline:assemble_transcripts (76)
[a7/4b6c37] Submitted process > pipeline:assemble_transcripts (79)
[42/eb0412] Submitted process > pipeline:assemble_transcripts (86)
[39/455421] Submitted process > pipeline:assemble_transcripts (77)
[e0/64e379] Submitted process > pipeline:assemble_transcripts (80)
[24/8631a3] Submitted process > pipeline:assemble_transcripts (78)
[90/56fcdf] Submitted process > pipeline:assemble_transcripts (81)
[10/5716d2] Submitted process > pipeline:assemble_transcripts (82)
[a6/2468fd] Submitted process > pipeline:assemble_transcripts (84)
[f4/e7d789] Submitted process > pipeline:assemble_transcripts (83)
[1a/512ce4] Submitted process > pipeline:assemble_transcripts (85)
[0b/d898e6] Submitted process > pipeline:assemble_transcripts (95)
[79/dc5637] Submitted process > pipeline:assemble_transcripts (87)
[4d/9332be] Submitted process > pipeline:assemble_transcripts (88)
[14/d2f142] Submitted process > pipeline:assemble_transcripts (89)
[de/74a129] Submitted process > pipeline:assemble_transcripts (99)
[b1/9e9b3a] Submitted process > pipeline:assemble_transcripts (90)
[8e/3afee8] Submitted process > pipeline:assemble_transcripts (91)
[14/e44f16] Submitted process > pipeline:assemble_transcripts (92)
[47/11a8b3] Submitted process > pipeline:assemble_transcripts (93)
[71/442cab] Submitted process > pipeline:assemble_transcripts (94)
[70/ef8956] Submitted process > pipeline:assemble_transcripts (103)
[e0/75d274] Submitted process > pipeline:assemble_transcripts (97)
[95/47afa4] Submitted process > pipeline:assemble_transcripts (96)
[83/656707] Submitted process > pipeline:assemble_transcripts (98)
[86/60b0ab] Submitted process > pipeline:assemble_transcripts (100)
[04/24e4ea] Submitted process > pipeline:assemble_transcripts (101)
[67/6de065] Submitted process > pipeline:assemble_transcripts (102)
[eb/bf583a] Submitted process > pipeline:assemble_transcripts (104)
[8e/fcc4ee] Submitted process > pipeline:assemble_transcripts (113)
[21/d8602c] Submitted process > pipeline:assemble_transcripts (115)
[54/d97da2] Submitted process > pipeline:assemble_transcripts (105)
[64/5506f7] Submitted process > pipeline:assemble_transcripts (106)
[5d/e27107] Submitted process > pipeline:assemble_transcripts (107)
[75/5864d2] Submitted process > pipeline:assemble_transcripts (108)
[ba/8b3c42] Submitted process > pipeline:assemble_transcripts (109)
[d2/dddb97] Submitted process > pipeline:assemble_transcripts (110)
[63/108f70] Submitted process > pipeline:assemble_transcripts (111)
[86/f30924] Submitted process > pipeline:assemble_transcripts (112)
[f4/dedde9] Submitted process > pipeline:assemble_transcripts (114)
[46/d7f336] Submitted process > pipeline:assemble_transcripts (116)
[19/f7f0d4] Submitted process > pipeline:assemble_transcripts (117)
[a5/1f93c1] Submitted process > pipeline:assemble_transcripts (118)
[c9/65afe6] Submitted process > pipeline:assemble_transcripts (128)
[f5/34acdd] Submitted process > pipeline:assemble_transcripts (119)
[39/eccce5] Submitted process > pipeline:assemble_transcripts (121)
[2f/997187] Submitted process > pipeline:assemble_transcripts (120)
[a6/3e887c] Submitted process > pipeline:assemble_transcripts (123)
[4e/a8d565] Submitted process > pipeline:assemble_transcripts (122)
[29/f00470] Submitted process > pipeline:assemble_transcripts (124)
[7e/88d7a0] Submitted process > pipeline:assemble_transcripts (125)
[e7/dcf249] Submitted process > pipeline:assemble_transcripts (126)
[16/a0e0f4] Submitted process > pipeline:assemble_transcripts (127)
[94/8ec7b0] Submitted process > pipeline:assemble_transcripts (129)
[93/2cfdac] Submitted process > pipeline:assemble_transcripts (132)
[52/da3d51] Submitted process > pipeline:assemble_transcripts (137)
[24/1dc4c6] Submitted process > pipeline:assemble_transcripts (141)
[ca/81306a] Submitted process > pipeline:assemble_transcripts (131)
[cf/6678f1] Submitted process > pipeline:assemble_transcripts (130)
[00/892bbd] Submitted process > pipeline:assemble_transcripts (133)
[74/fbd5d1] Submitted process > pipeline:assemble_transcripts (144)
[23/c8d7c4] Submitted process > pipeline:assemble_transcripts (145)
[9a/36aab5] Submitted process > pipeline:assemble_transcripts (134)
[ea/7f4ed1] Submitted process > pipeline:assemble_transcripts (138)
[bf/5afa94] Submitted process > pipeline:assemble_transcripts (135)
[0d/4264c0] Submitted process > pipeline:assemble_transcripts (139)
[30/af21b3] Submitted process > pipeline:assemble_transcripts (136)
[dc/5e6c29] Submitted process > pipeline:assemble_transcripts (140)
[71/4cf06c] Submitted process > pipeline:assemble_transcripts (142)
[0e/8659ce] Submitted process > pipeline:assemble_transcripts (143)
[19/a2bebe] Submitted process > pipeline:assemble_transcripts (146)
[4e/a16dcf] Submitted process > pipeline:assemble_transcripts (150)
[08/c97b4a] Submitted process > pipeline:assemble_transcripts (147)
[ad/f4a1c2] Submitted process > pipeline:assemble_transcripts (148)
[e2/16a43d] Submitted process > pipeline:assemble_transcripts (149)
[68/4754be] Submitted process > pipeline:merge_gff_bundles (1)
[3d/99d9a3] Submitted process > pipeline:run_gffcompare (1)
ERROR ~ Error executing process > 'pipeline:run_gffcompare (1)'
Caused by:
  Process `pipeline:run_gffcompare (1)` terminated with an error exit status (1)
Command executed:
  mkdir calls_yki
  echo "Doing comparison of reference annotation: amended.Drosophila_melanogaster.BDGP6.46.112.filtered.EGFP.gtf and the query annotation"
  
  gffcompare -o calls_yki/str_merged -r amended.Drosophila_melanogaster.BDGP6.46.112.filtered.EGFP.gtf             -R calls_yki.gff
  
  mv *.tmap "calls_yki"
  mv *.refmap "calls_yki"
  cp "calls_yki/str_merged.annotated.gtf" "calls_yki_annotated.gtf"
  
  workflow-glue parse_gffcompare             --sample_id "calls_yki"             --gffcompare_dir "calls_yki"             --isoform_table_out "calls_yki_transcripts_table.tsv"             --tracking calls_yki/str_merged.tracking             --annotation amended.Drosophila_melanogaster.BDGP6.46.112.filtered.EGFP.gtf
Command exit status:
  1
Command output:
  Doing comparison of reference annotation: amended.Drosophila_melanogaster.BDGP6.46.112.filtered.EGFP.gtf and the query annotation
Command error:
    20350 query transfrags loaded.
  [16:13:36 - workflow_glue] Bootstrapping CLI.
  [16:13:37 - workflow_glue] Starting entrypoint.
  /opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/util/_decorators.py:311: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.
    return func(*args, **kwargs)
  Traceback (most recent call last):
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3361, in get_loc
      return self._engine.get_loc(casted_key)
    File "pandas/_libs/index.pyx", line 76, in pandas._libs.index.IndexEngine.get_loc
    File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
    File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
    File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
  KeyError: nan
  
  The above exception was the direct cause of the following exception:
  
  Traceback (most recent call last):
    File "/home/drsc-linux/epi2melabs/workflows/epi2me-labs/wf-transcriptomes/bin/workflow-glue", line 7, in <module>
      cli()
    File "/home/drsc-linux/epi2melabs/workflows/epi2me-labs/wf-transcriptomes/bin/workflow_glue/__init__.py", line 82, in cli
      args.func(args)
    File "/home/drsc-linux/epi2melabs/workflows/epi2me-labs/wf-transcriptomes/bin/workflow_glue/parse_gffcompare.py", line 260, in main
      make_isoform_table(args.gffcompare_dir, args.sample_id, args.isoform_table_out)
    File "/home/drsc-linux/epi2melabs/workflows/epi2me-labs/wf-transcriptomes/bin/workflow_glue/parse_gffcompare.py", line 246, in make_isoform_table
      df['parent gene iso num'] = df.apply(
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/frame.py", line 8740, in apply
      return op.apply()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/apply.py", line 688, in apply
      return self.apply_standard()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/apply.py", line 812, in apply_standard
      results, res_index = self.apply_series_generator()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/apply.py", line 828, in apply_series_generator
      results[i] = self.f(v)
    File "/home/drsc-linux/epi2melabs/workflows/epi2me-labs/wf-transcriptomes/bin/workflow_glue/parse_gffcompare.py", line 247, in <lambda>
      lambda x: gb.loc[(x.ref_gene_id), 'num_isoforms'], axis=1)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 925, in __getitem__
      return self._getitem_tuple(key)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 1100, in _getitem_tuple
      return self._getitem_lowerdim(tup)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 838, in _getitem_lowerdim
      section = self._getitem_axis(key, axis=i)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 1164, in _getitem_axis
      return self._get_label(key, axis=axis)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 1113, in _get_label
      return self.obj.xs(label, axis=axis)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/generic.py", line 3776, in xs
      loc = index.get_loc(key)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3363, in get_loc
      raise KeyError(key) from err
  KeyError: nan
Work dir:
  /home/drsc-linux/epi2melabs/instances/wf-transcriptomes_01JDMCDRBMWF71F0DR3HJDM0S8/work/3d/99d9a3dd6a21a1abefb99252a4d2b3
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 -- Check '/home/drsc-linux/epi2melabs/instances/wf-transcriptomes_01JDMCDRBMWF71F0DR3HJDM0S8/nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response
@nrhorner
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nrhorner commented Dec 1, 2024

Hi @mujeebqadiri6308

Sorry that your having issues with the workflow. Would you be able to rerun with a previous version of the workflow 1.4.0 -r v1.4.0 and see if you still encounter this problem?

@nrhorner
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nrhorner commented Dec 1, 2024

@mujeebqadiri6308, are you be able to share the file: /home/drsc-linux/epi2melabs/instances/wf-transcriptomes_01JDMCDRBMWF71F0DR3HJDM0S8/work/3d/99d9a3dd6a21a1abefb99252a4d2b3/calls_yki/str_merged.tracking ?

@mujeebqadiri6308
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@mujeebqadiri6308, are you be able to share the file: /home/drsc-linux/epi2melabs/instances/wf-transcriptomes_01JDMCDRBMWF71F0DR3HJDM0S8/work/3d/99d9a3dd6a21a1abefb99252a4d2b3/calls_yki/str_merged.tracking ?

Hi, thank you for the reply! I can share the file, is there an email that I may send it to? Also I have tried an earlier version of the workflow and also received an error, I will re-run it with v1.4.0 and post the error (I believe it was the same).

@nrhorner
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nrhorner commented Dec 6, 2024

@mujeebqadiri6308 I believe I just found you on LinkedIn. If you could drop me your email address there, I can give you access to a cloud folder to upload it to.

Thanks,

Neil

@MujeebQadiri
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@mujeebqadiri6308 I believe I just found you on LinkedIn. If you could drop me your email address there, I can give you access to a cloud folder to upload it to.

Thanks,

Neil

Hi Neil,

Thank you, I have sent you a connect request (as I cannot message you on linked-in without first connecting).

Best,
Mujeeb

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@nrhorner @MujeebQadiri @mujeebqadiri6308