ValueError: Flu type is undetermined

[Oliversinn]

Operating System

Windows 10

Other Linux

No response

Workflow Version

v1.1.0

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

v5.1.14

CLI command run

nextflow run epi2me-labs/wf-flu --rbk --fastq ./fastq/pass/ --disable_ping --out_dir resultado/

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Workflow crashes at pipeline:prepNextclade. I think handling the error is correct:

ERROR ~ Error executing process > 'pipeline:prepNextclade (24)'
Caused by:
  Process `pipeline:prepNextclade (24)` terminated with an error exit status (1)
Command executed:
  mkdir datasets
  workflow-glue nextclade_helper         --typing typing.json         --nextclade_datasets "nextclade_data"         --consensus "consensus.fasta"         --sample_alias "barcode31"
  
  if [ -z "$(ls -A datasets)" ]; then
      rm -r datasets
  fi
Command exit status:
  1
Command output:
  (empty)
Command error:
  [02:20:44 - matplotlib.font_manager] generated new fontManager
  [02:20:45 - workflow_glue] Starting entrypoint.
  Traceback (most recent call last):
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow-glue", line 7, in <module>
      cli()
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/__init__.py", line 72, in cli
      args.func(args)
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/nextclade_helper.py", line 88, in main
      datasets = find_nextclade(typing, args.nextclade_datasets)
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/nextclade_helper.py", line 40, in find_nextclade
      raise ValueError("Flu type is undetermined. \n \
  ValueError: Flu type is undetermined. 
                                If reads are from the RBK protocol, ensure                              --rbk has been set to prevent overfiltering.

But I think it should let the workflow to continue and just flag the barcode that contains the error in the report. I have 95 barcodes, and in every iteration I removed the barcode's folder mentioned in the log (above is barcode31) in order to avoid the whole workflow to crash.

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/main.nf` [hardcore_archimedes] DSL2 - revision: 71a74190d7
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-flu v1.1.0
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : hardcore_archimedes
  containerEngine: docker
  launchDir      : /mnt/c/Users/labor/epi2melabs/instances/wf-flu_01HZZXQD874N2MSF91QF64ZK2N
  workDir        : /mnt/c/Users/labor/epi2melabs/instances/wf-flu_01HZZXQD874N2MSF91QF64ZK2N/work
  projectDir     : /mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu
  userName       : epi2mewsl
  profile        : standard
  configFiles    : /mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/nextflow.config, /mnt/c/Users/labor/epi2melabs/instances/wf-flu_01HZZXQD874N2MSF91QF64ZK2N/local.config
Input Options
  fastq          : /mnt/c/data/SeqInfluenzaAMayo2024/no_sample/20240514_1842_MN37814_FAY07468_2be73a9e/fastq/pass - Copy
Output Options
  out_dir        : /mnt/c/Users/labor/epi2melabs/instances/wf-flu_01HZZXQD874N2MSF91QF64ZK2N/output
Miscellaneous Options
  disable_ping   : true
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-flu for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-flu v1.1.0.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
NOT Downsampling!!!
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[3d/b2f84f] Submitted process > pipeline:coverageCalc (63)
[9a/fdab8e] Submitted process > pipeline:medakaVariants (63)
[90/df9e87] Submitted process > pipeline:coverageCalc (64)
[50/a46d92] Submitted process > pipeline:medakaVariants (64)
[6c/2ad912] Submitted process > pipeline:coverageCalc (65)
[87/372933] Submitted process > pipeline:medakaVariants (65)
[d3/28e745] Submitted process > pipeline:coverageCalc (66)
[4b/e88931] Submitted process > pipeline:medakaVariants (66)
[9e/798816] Submitted process > pipeline:coverageCalc (67)
[12/813a42] Submitted process > pipeline:medakaVariants (67)
[7e/9071e2] Submitted process > pipeline:coverageCalc (68)
[07/3d237a] Submitted process > pipeline:medakaVariants (68)
[23/389cc5] Submitted process > pipeline:coverageCalc (69)
[73/974989] Submitted process > pipeline:medakaVariants (69)
[0a/c00d19] Submitted process > pipeline:coverageCalc (70)
[3c/c7ede4] Submitted process > pipeline:medakaVariants (70)
[8d/e43d3e] Submitted process > pipeline:coverageCalc (71)
[09/ae7c91] Submitted process > pipeline:medakaVariants (71)
[b3/047658] Submitted process > pipeline:coverageCalc (72)
[2c/b45595] Submitted process > pipeline:medakaVariants (72)
[74/94011b] Submitted process > pipeline:coverageCalc (73)
[e2/bc5bcb] Submitted process > pipeline:medakaVariants (73)
[25/184757] Submitted process > pipeline:coverageCalc (74)
[60/10517f] Submitted process > pipeline:medakaVariants (74)
[10/691327] Submitted process > pipeline:coverageCalc (75)
[05/34ca69] Submitted process > pipeline:medakaVariants (75)
[f2/f569af] Submitted process > pipeline:coverageCalc (76)
[6e/4d6dc5] Submitted process > pipeline:medakaVariants (76)
[8f/b45b81] Submitted process > pipeline:coverageCalc (77)
[80/1bcf5f] Submitted process > pipeline:medakaVariants (77)
[36/c3980e] Submitted process > pipeline:coverageCalc (78)
[da/233181] Submitted process > pipeline:medakaVariants (78)
[26/3e9829] Submitted process > pipeline:coverageCalc (79)
[f3/62fcc2] Submitted process > pipeline:medakaVariants (79)
[85/9599c1] Submitted process > pipeline:coverageCalc (80)
[79/8395f6] Submitted process > pipeline:medakaVariants (80)
[90/9da790] Submitted process > pipeline:coverageCalc (81)
[14/3a57d1] Submitted process > pipeline:medakaVariants (81)
[2e/69f363] Submitted process > pipeline:coverageCalc (82)
[e3/88ad37] Submitted process > pipeline:medakaVariants (82)
[63/9fb91c] Submitted process > pipeline:coverageCalc (83)
[af/c7a2ff] Submitted process > pipeline:medakaVariants (83)
[e3/697fb5] Submitted process > pipeline:coverageCalc (84)
[5c/ad256c] Submitted process > pipeline:medakaVariants (84)
[6e/68ab16] Submitted process > pipeline:coverageCalc (85)
[26/9d2bd1] Submitted process > pipeline:medakaVariants (85)
[4e/d21d13] Submitted process > pipeline:coverageCalc (86)
[5b/f45bc8] Submitted process > pipeline:medakaVariants (86)
[88/4d8b07] Submitted process > pipeline:medakaVariants (87)
[e3/79371a] Submitted process > pipeline:coverageCalc (87)
[60/038b76] Submitted process > pipeline:coverageCalc (88)
[a2/0e92b2] Submitted process > pipeline:medakaVariants (88)
[cb/49a473] Submitted process > pipeline:coverageCalc (89)
[6b/97f45d] Submitted process > pipeline:medakaVariants (89)
[7f/09cc98] Submitted process > pipeline:makeConsensus (1)
[7e/c83247] Submitted process > pipeline:coverageCalc (90)
[22/ae3342] Submitted process > pipeline:medakaVariants (90)
[47/1f38f4] Submitted process > pipeline:makeConsensus (2)
[b6/e2528a] Submitted process > pipeline:makeConsensus (3)
[16/71e32f] Submitted process > pipeline:makeConsensus (4)
[88/e9523d] Submitted process > pipeline:makeConsensus (5)
[ac/66520f] Submitted process > pipeline:makeConsensus (6)
[59/d0fa3d] Submitted process > pipeline:makeConsensus (7)
[91/ab8cec] Submitted process > pipeline:makeConsensus (8)
[bc/ad210e] Submitted process > pipeline:makeConsensus (9)
[9b/7cfe9e] Submitted process > pipeline:makeConsensus (10)
[a4/498e45] Submitted process > pipeline:makeConsensus (11)
[da/0e2a4e] Submitted process > pipeline:makeConsensus (12)
[74/a3d6f5] Submitted process > pipeline:makeConsensus (13)
[85/c6f753] Submitted process > pipeline:makeConsensus (14)
[f7/1b3664] Submitted process > pipeline:coverageCalc (91)
[72/7afc40] Submitted process > pipeline:medakaVariants (91)
[32/4a87a2] Submitted process > pipeline:makeConsensus (15)
[16/59c4fd] Submitted process > pipeline:makeConsensus (16)
[aa/b92413] Submitted process > pipeline:makeConsensus (17)
[da/107a89] Submitted process > pipeline:makeConsensus (18)
[21/1a61e6] Submitted process > pipeline:makeConsensus (19)
[35/877ee3] Submitted process > pipeline:makeConsensus (20)
[b4/53026e] Submitted process > pipeline:makeConsensus (21)
[47/6c2836] Submitted process > pipeline:makeConsensus (22)
[30/6ef6a9] Submitted process > pipeline:makeConsensus (23)
[ca/88669f] Submitted process > pipeline:makeConsensus (24)
[d0/5cd28c] Submitted process > pipeline:coverageCalc (92)
[e6/2f6c3f] Submitted process > pipeline:medakaVariants (92)
[51/476460] Submitted process > pipeline:makeConsensus (25)
[03/95fe9a] Submitted process > pipeline:makeConsensus (26)
[f1/fb562e] Submitted process > pipeline:makeConsensus (27)
[a6/247d8b] Submitted process > pipeline:makeConsensus (28)
[b6/0e9938] Submitted process > pipeline:coverageCalc (93)
[6b/6f6b19] Submitted process > pipeline:medakaVariants (93)
[a2/05a73b] Submitted process > pipeline:makeConsensus (29)
[cd/0370dd] Submitted process > pipeline:makeConsensus (30)
[7b/75d3f0] Submitted process > pipeline:makeConsensus (31)
[7b/87d764] Submitted process > pipeline:makeConsensus (32)
[35/7c2afe] Submitted process > pipeline:makeConsensus (33)
[df/b0f17d] Submitted process > pipeline:makeConsensus (34)
[63/ce14a5] Submitted process > pipeline:coverageCalc (94)
[ff/aa4451] Submitted process > pipeline:medakaVariants (94)
[5c/22d710] Submitted process > pipeline:makeConsensus (35)
[4f/64e3f8] Submitted process > pipeline:makeConsensus (36)
[8d/1013a4] Submitted process > pipeline:makeConsensus (37)
[64/06e8d2] Submitted process > pipeline:makeConsensus (38)
[16/25851b] Submitted process > pipeline:makeConsensus (39)
[fc/d7c0ba] Submitted process > pipeline:makeConsensus (40)
[35/42135f] Submitted process > pipeline:makeConsensus (41)
[9b/89b946] Submitted process > pipeline:makeConsensus (42)
[9a/b0e580] Submitted process > pipeline:makeConsensus (43)
[6d/ffa39c] Submitted process > pipeline:makeConsensus (44)
[fe/b797c7] Submitted process > pipeline:makeConsensus (45)
[8d/d5c6ca] Submitted process > pipeline:makeConsensus (46)
[db/e7c159] Submitted process > pipeline:makeConsensus (47)
[6a/578bfe] Submitted process > pipeline:makeConsensus (48)
[d0/c99394] Submitted process > pipeline:makeConsensus (49)
[fd/5b8cc9] Submitted process > pipeline:makeConsensus (50)
[2e/b33a96] Submitted process > pipeline:makeConsensus (51)
[81/68e473] Submitted process > pipeline:makeConsensus (52)
[dc/ecf6ba] Submitted process > pipeline:makeConsensus (53)
[90/e34b62] Submitted process > pipeline:makeConsensus (54)
[a0/1cec74] Submitted process > pipeline:makeConsensus (55)
[68/bc0667] Submitted process > pipeline:makeConsensus (56)
[a5/57d828] Submitted process > pipeline:makeConsensus (57)
[60/0719f5] Submitted process > pipeline:makeConsensus (58)
[81/4e1ee6] Submitted process > pipeline:makeConsensus (59)
[88/e10c74] Submitted process > pipeline:makeConsensus (60)
[32/e452f9] Submitted process > pipeline:makeConsensus (61)
[62/5f552d] Submitted process > pipeline:makeConsensus (62)
[3e/bb094a] Submitted process > pipeline:makeConsensus (63)
[81/cbd88f] Submitted process > pipeline:makeConsensus (64)
[0a/fffe6d] Submitted process > pipeline:makeConsensus (65)
[b8/33e72d] Submitted process > pipeline:makeConsensus (66)
[bc/4fe5c6] Submitted process > pipeline:makeConsensus (67)
[85/5d363b] Submitted process > pipeline:makeConsensus (68)
[f4/6782c8] Submitted process > pipeline:makeConsensus (69)
[ea/3d45bf] Submitted process > pipeline:makeConsensus (70)
[02/e719e7] Submitted process > pipeline:makeConsensus (71)
[40/d973e1] Submitted process > pipeline:makeConsensus (72)
[22/478a55] Submitted process > pipeline:makeConsensus (73)
[f5/ffcea1] Submitted process > pipeline:makeConsensus (74)
[f6/b6c2a4] Submitted process > pipeline:makeConsensus (75)
[9b/f21e34] Submitted process > pipeline:makeConsensus (76)
[f9/16923b] Submitted process > pipeline:typeFlu (1)
[87/752898] Submitted process > pipeline:makeConsensus (77)
[c7/d5f3e6] Submitted process > pipeline:typeFlu (2)
[08/f5828a] Submitted process > pipeline:typeFlu (3)
[53/9f0fa7] Submitted process > pipeline:typeFlu (4)
[7a/8e1de5] Submitted process > pipeline:makeConsensus (78)
[42/f55e66] Submitted process > pipeline:typeFlu (5)
[f0/322ea7] Submitted process > pipeline:typeFlu (6)
[50/7be334] Submitted process > pipeline:makeConsensus (79)
[f7/0f71d8] Submitted process > pipeline:makeConsensus (80)
[06/51bd56] Submitted process > pipeline:typeFlu (7)
[1b/0ce57a] Submitted process > pipeline:typeFlu (8)
[f3/3eb954] Submitted process > pipeline:typeFlu (9)
[dc/76343c] Submitted process > pipeline:makeConsensus (81)
[ca/cd2abe] Submitted process > pipeline:typeFlu (10)
[98/be1e63] Submitted process > pipeline:typeFlu (11)
[7c/49f2dd] Submitted process > pipeline:typeFlu (12)
[97/5763c7] Submitted process > pipeline:typeFlu (13)
[fc/463203] Submitted process > pipeline:typeFlu (14)
[f8/cebffa] Submitted process > pipeline:typeFlu (15)
[76/08ee1f] Submitted process > pipeline:typeFlu (16)
[1c/43a52e] Submitted process > pipeline:typeFlu (17)
[31/ee9cc8] Submitted process > pipeline:makeConsensus (82)
[f5/be48d9] Submitted process > pipeline:typeFlu (18)
[3b/82eb86] Submitted process > pipeline:typeFlu (19)
[23/89b27b] Submitted process > pipeline:typeFlu (20)
[1b/bcb957] Submitted process > pipeline:typeFlu (21)
[18/bbefc6] Submitted process > pipeline:typeFlu (22)
[d8/e4d6d2] Submitted process > pipeline:typeFlu (23)
[06/3709df] Submitted process > pipeline:typeFlu (24)
[9e/280430] Submitted process > pipeline:typeFlu (25)
[97/018ad8] Submitted process > pipeline:typeFlu (26)
[99/599eb3] Submitted process > pipeline:typeFlu (27)
[ab/ad3c78] Submitted process > pipeline:typeFlu (28)
[19/dfc033] Submitted process > pipeline:makeConsensus (83)
[ec/c60b4d] Submitted process > pipeline:typeFlu (29)
[2c/b5a099] Submitted process > pipeline:typeFlu (30)
[8a/e7eb3f] Submitted process > pipeline:typeFlu (31)
[0c/218974] Submitted process > pipeline:typeFlu (32)
[4a/ca4a5c] Submitted process > pipeline:typeFlu (33)
[74/076be6] Submitted process > pipeline:typeFlu (34)
[49/bf32c4] Submitted process > pipeline:makeConsensus (84)
[2c/00adbc] Submitted process > pipeline:typeFlu (35)
[b5/d6f6dc] Submitted process > pipeline:typeFlu (36)
[eb/f1fa84] Submitted process > pipeline:typeFlu (37)
[8d/b0244e] Submitted process > pipeline:typeFlu (38)
[d1/6aa005] Submitted process > pipeline:typeFlu (39)
[d1/6857e0] Submitted process > pipeline:typeFlu (40)
[d6/073c13] Submitted process > pipeline:typeFlu (41)
[ff/497384] Submitted process > pipeline:typeFlu (42)
[a4/76f958] Submitted process > pipeline:typeFlu (43)
[5a/7afb98] Submitted process > pipeline:makeConsensus (85)
[4f/c9e7db] Submitted process > pipeline:typeFlu (44)
[18/aa6307] Submitted process > pipeline:typeFlu (45)
[01/6ef8df] Submitted process > pipeline:typeFlu (46)
[38/72fc4b] Submitted process > pipeline:typeFlu (47)
[f8/beb8a1] Submitted process > pipeline:typeFlu (48)
[5b/45a300] Submitted process > pipeline:typeFlu (49)
[11/726445] Submitted process > pipeline:typeFlu (50)
[8e/324644] Submitted process > pipeline:makeConsensus (86)
[bc/641c28] Submitted process > pipeline:typeFlu (51)
[7b/f9ee31] Submitted process > pipeline:typeFlu (52)
[32/fff0b0] Submitted process > pipeline:typeFlu (53)
[82/444ecc] Submitted process > pipeline:typeFlu (54)
[d4/5e8c83] Submitted process > pipeline:typeFlu (55)
[e5/520e43] Submitted process > pipeline:typeFlu (56)
[56/e26acd] Submitted process > pipeline:typeFlu (57)
[79/f00ca0] Submitted process > pipeline:typeFlu (58)
[3f/32760f] Submitted process > pipeline:typeFlu (59)
[9c/368177] Submitted process > pipeline:typeFlu (60)
[98/d7a54b] Submitted process > pipeline:typeFlu (61)
[8d/8bc01f] Submitted process > pipeline:typeFlu (62)
[d0/6dcc0d] Submitted process > pipeline:typeFlu (63)
[01/345ba4] Submitted process > pipeline:typeFlu (64)
[ee/4a2eb3] Submitted process > pipeline:typeFlu (65)
[af/2ad774] Submitted process > pipeline:typeFlu (66)
[ea/651bb5] Submitted process > pipeline:typeFlu (67)
[0f/48b100] Submitted process > pipeline:typeFlu (68)
[5a/f84ac5] Submitted process > pipeline:typeFlu (69)
[9c/071f5c] Submitted process > pipeline:typeFlu (70)
[2a/427e6f] Submitted process > pipeline:typeFlu (71)
[ef/cf43e8] Submitted process > pipeline:typeFlu (72)
[1a/a66df3] Submitted process > pipeline:typeFlu (73)
[61/e96e96] Submitted process > pipeline:typeFlu (74)
[ba/594adb] Submitted process > pipeline:typeFlu (75)
[6f/0e47e6] Submitted process > pipeline:typeFlu (76)
[53/1f6d23] Submitted process > pipeline:processType (1)
[32/055858] Submitted process > pipeline:typeFlu (77)
[67/04cd46] Submitted process > pipeline:processType (2)
[94/1951b9] Submitted process > pipeline:processType (3)
[e8/96e055] Submitted process > pipeline:processType (4)
[dd/aa4e82] Submitted process > pipeline:processType (5)
[19/857ec5] Submitted process > pipeline:typeFlu (78)
[73/5403e4] Submitted process > pipeline:processType (6)
[b8/f0a609] Submitted process > pipeline:typeFlu (79)
[55/9e4c1c] Submitted process > pipeline:typeFlu (80)
[14/0d1264] Submitted process > pipeline:processType (7)
[50/f966c8] Submitted process > pipeline:processType (8)
[e2/70cb56] Submitted process > pipeline:processType (9)
[3f/57c71e] Submitted process > pipeline:typeFlu (81)
[24/bf6044] Submitted process > pipeline:processType (10)
[71/af3383] Submitted process > pipeline:processType (11)
[72/041244] Submitted process > pipeline:processType (12)
[a0/6fad15] Submitted process > pipeline:processType (13)
[98/f22f4c] Submitted process > pipeline:processType (14)
[fb/fe375b] Submitted process > pipeline:processType (15)
[16/4cfa17] Submitted process > pipeline:processType (16)
[25/4b7ffe] Submitted process > pipeline:processType (17)
[c9/4604b7] Submitted process > pipeline:processType (18)
[28/4a1024] Submitted process > pipeline:typeFlu (82)
[e0/83d4ee] Submitted process > pipeline:processType (19)
[6c/feece6] Submitted process > pipeline:processType (20)
[60/2bc195] Submitted process > pipeline:processType (21)
[a0/851dda] Submitted process > pipeline:processType (22)
[68/6a9c2b] Submitted process > pipeline:processType (23)
[93/d950d0] Submitted process > pipeline:processType (24)
[38/4701ee] Submitted process > pipeline:processType (25)
[85/921bf4] Submitted process > pipeline:processType (26)
[bc/fad792] Submitted process > pipeline:processType (27)
[42/ceb6fc] Submitted process > pipeline:processType (28)
[23/d94e46] Submitted process > pipeline:processType (29)
[37/921bcb] Submitted process > pipeline:typeFlu (83)
[3f/59cf4c] Submitted process > pipeline:processType (30)
[ed/de60f0] Submitted process > pipeline:processType (31)
[43/de40d3] Submitted process > pipeline:processType (32)
[c7/144943] Submitted process > pipeline:processType (33)
[f7/d39670] Submitted process > pipeline:processType (34)
[19/1d8603] Submitted process > pipeline:typeFlu (84)
[3c/d2b2dc] Submitted process > pipeline:processType (35)
[de/9a0029] Submitted process > pipeline:processType (36)
[af/feee93] Submitted process > pipeline:processType (37)
[7b/4d51b7] Submitted process > pipeline:processType (38)
[d2/09b308] Submitted process > pipeline:processType (39)
[31/930abb] Submitted process > pipeline:processType (40)
[e0/b417a5] Submitted process > pipeline:processType (41)
[6c/f58941] Submitted process > pipeline:processType (42)
[a9/9886a5] Submitted process > pipeline:processType (43)
[9b/ce501e] Submitted process > pipeline:typeFlu (85)
[72/4dd0c0] Submitted process > pipeline:processType (44)
[d1/83d089] Submitted process > pipeline:processType (45)
[64/c175e1] Submitted process > pipeline:processType (46)
[30/9fc0ee] Submitted process > pipeline:processType (47)
[94/6d4f14] Submitted process > pipeline:processType (48)
[d2/7fab71] Submitted process > pipeline:processType (49)
[8c/2c13e7] Submitted process > pipeline:processType (50)
[cf/e2d7f7] Submitted process > pipeline:processType (51)
[11/ee9bed] Submitted process > pipeline:typeFlu (86)
[17/bd1e2d] Submitted process > pipeline:processType (52)
[70/d2e3fe] Submitted process > pipeline:processType (53)
[46/8f1aa5] Submitted process > pipeline:processType (54)
[c9/8982de] Submitted process > pipeline:processType (55)
[91/2e77fc] Submitted process > pipeline:processType (56)
[93/f81812] Submitted process > pipeline:processType (57)
[60/d701f9] Submitted process > pipeline:processType (58)
[be/c20079] Submitted process > pipeline:processType (59)
[d5/b7d910] Submitted process > pipeline:processType (60)
[11/d218e4] Submitted process > pipeline:processType (61)
[a0/85fc21] Submitted process > pipeline:processType (62)
[39/7b517a] Submitted process > pipeline:processType (63)
[81/3cb253] Submitted process > pipeline:processType (64)
[37/5b787c] Submitted process > pipeline:processType (65)
[78/3350ce] Submitted process > pipeline:processType (66)
[92/c5207a] Submitted process > pipeline:processType (67)
[5d/83dcb1] Submitted process > pipeline:processType (68)
[38/5244cd] Submitted process > pipeline:processType (69)
[c4/440d6d] Submitted process > pipeline:processType (70)
[25/9f2545] Submitted process > pipeline:processType (71)
[c4/4d89fe] Submitted process > pipeline:processType (72)
[62/12ecce] Submitted process > pipeline:processType (73)
[64/c73779] Submitted process > pipeline:processType (74)
[a5/14182c] Submitted process > pipeline:processType (75)
[99/f03cef] Submitted process > pipeline:processType (76)
[b4/761606] Submitted process > pipeline:processType (77)
[26/61f76f] Submitted process > pipeline:processType (78)
[ca/4edadf] Submitted process > pipeline:prepNextclade (1)
[5c/11e1f1] Submitted process > pipeline:collectFilesInDir (1)
[01/ca971d] Submitted process > pipeline:prepNextclade (2)
[4f/9584b4] Submitted process > pipeline:collectFilesInDir (2)
[79/ade915] Submitted process > pipeline:prepNextclade (3)
[85/203fb3] Submitted process > pipeline:collectFilesInDir (3)
[b5/3d2260] Submitted process > pipeline:processType (79)
[d2/8f78a3] Submitted process > pipeline:prepNextclade (4)
[28/fa3d2e] Submitted process > pipeline:collectFilesInDir (4)
[e6/33505a] Submitted process > pipeline:prepNextclade (5)
[ae/262d2e] Submitted process > pipeline:collectFilesInDir (5)
[67/9946b0] Submitted process > pipeline:processType (80)
[49/34230b] Submitted process > pipeline:prepNextclade (6)
[ed/546ad3] Submitted process > pipeline:collectFilesInDir (6)
[8b/0dad71] Submitted process > pipeline:processType (81)
[09/54e8de] Submitted process > pipeline:makeConsensus (87)
[b1/f6d483] Submitted process > pipeline:prepNextclade (7)
[05/042fd9] Submitted process > pipeline:collectFilesInDir (7)
[89/c6e4da] Submitted process > pipeline:prepNextclade (8)
[91/68383f] Submitted process > pipeline:collectFilesInDir (8)
[03/5582bd] Submitted process > pipeline:prepNextclade (9)
[5f/84b475] Submitted process > pipeline:collectFilesInDir (9)
[c3/a2006b] Submitted process > pipeline:prepNextclade (10)
[f2/4abcb1] Submitted process > pipeline:collectFilesInDir (10)
[0a/0c1346] Submitted process > pipeline:prepNextclade (11)
[42/7ef476] Submitted process > pipeline:collectFilesInDir (11)
[00/7722b5] Submitted process > pipeline:prepNextclade (12)
[f3/c41e8a] Submitted process > pipeline:collectFilesInDir (12)
[5f/55ee37] Submitted process > pipeline:processType (82)
[f5/d65580] Submitted process > pipeline:prepNextclade (13)
[d6/1ca1c3] Submitted process > pipeline:collectFilesInDir (13)
[4a/e5f3cf] Submitted process > pipeline:prepNextclade (14)
[e8/5305ec] Submitted process > pipeline:collectFilesInDir (14)
[7a/05753e] Submitted process > pipeline:prepNextclade (15)
[a3/3ad46b] Submitted process > pipeline:collectFilesInDir (15)
[28/f6595f] Submitted process > pipeline:prepNextclade (16)
[76/e2af4c] Submitted process > pipeline:collectFilesInDir (16)
[04/c227ac] Submitted process > pipeline:prepNextclade (17)
[74/f13cb1] Submitted process > pipeline:collectFilesInDir (17)
[b6/0004ea] Submitted process > pipeline:prepNextclade (18)
[84/036595] Submitted process > pipeline:collectFilesInDir (18)
[87/0d98d2] Submitted process > pipeline:prepNextclade (19)
[e7/e5a8fb] Submitted process > pipeline:collectFilesInDir (19)
[e9/edcc82] Submitted process > pipeline:prepNextclade (20)
[e8/68375b] Submitted process > pipeline:collectFilesInDir (20)
[a2/01b9e4] Submitted process > pipeline:prepNextclade (21)
[1f/bbebb1] Submitted process > pipeline:collectFilesInDir (21)
[e1/3b41d0] Submitted process > pipeline:prepNextclade (22)
[5a/fbda06] Submitted process > pipeline:collectFilesInDir (22)
[09/eb7bb5] Submitted process > pipeline:prepNextclade (23)
[88/92f468] Submitted process > pipeline:collectFilesInDir (23)
[6d/5e969d] Submitted process > pipeline:prepNextclade (24)
[9e/6fe54d] Submitted process > pipeline:collectFilesInDir (24)
[a1/789ecc] Submitted process > pipeline:prepNextclade (25)
[cb/b00e7b] Submitted process > pipeline:collectFilesInDir (25)
[c2/11d9c1] Submitted process > pipeline:processType (83)
[a6/ced1e0] Submitted process > pipeline:prepNextclade (26)
[50/dd0740] Submitted process > pipeline:collectFilesInDir (26)
[7c/4ce65c] Submitted process > pipeline:prepNextclade (27)
[c2/b5e0aa] Submitted process > pipeline:collectFilesInDir (27)
[2c/8ce917] Submitted process > pipeline:prepNextclade (28)
[fa/fb4817] Submitted process > pipeline:collectFilesInDir (28)
[4d/ae2988] Submitted process > pipeline:prepNextclade (29)
[1d/262cb5] Submitted process > pipeline:collectFilesInDir (29)
[7b/d5b97b] Submitted process > pipeline:prepNextclade (30)
[b5/a3f601] Submitted process > pipeline:collectFilesInDir (30)
[0f/9591c3] Submitted process > pipeline:prepNextclade (31)
ERROR ~ Error executing process > 'pipeline:prepNextclade (24)'
Caused by:
  Process `pipeline:prepNextclade (24)` terminated with an error exit status (1)
Command executed:
  mkdir datasets
  workflow-glue nextclade_helper         --typing typing.json         --nextclade_datasets "nextclade_data"         --consensus "consensus.fasta"         --sample_alias "barcode31"
  
  if [ -z "$(ls -A datasets)" ]; then
      rm -r datasets
  fi
Command exit status:
  1
Command output:
  (empty)
Command error:
  [02:20:44 - matplotlib.font_manager] generated new fontManager
  [02:20:45 - workflow_glue] Starting entrypoint.
  Traceback (most recent call last):
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow-glue", line 7, in <module>
      cli()
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/__init__.py", line 72, in cli
      args.func(args)
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/nextclade_helper.py", line 88, in main
      datasets = find_nextclade(typing, args.nextclade_datasets)
    File "/mnt/c/Users/labor/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/nextclade_helper.py", line 40, in find_nextclade
      raise ValueError("Flu type is undetermined. \n \
  ValueError: Flu type is undetermined. 
                                If reads are from the RBK protocol, ensure                              --rbk has been set to prevent overfiltering.
Work dir:
  /mnt/c/Users/labor/epi2melabs/instances/wf-flu_01HZZXQD874N2MSF91QF64ZK2N/work/6d/5e969d18093cb4ab72d0cfd39677c5
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
 -- Check '/mnt/c/Users/labor/epi2melabs/instances/wf-flu_01HZZXQD874N2MSF91QF64ZK2N/nextflow.log' file for details
WARN: Killing running tasks (14)

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

[cjalder]

Hi @Oliversinn - Thanks for flagging the issue. I agree the workflow should catch this exception and continue with the rest of the workflow. We are currently working on a fix to allow this to happen!

[forty2wallabyway]

Edit: Deleted original comment also asking for help. Found solution:

Adding the following line to main.nf into prepNextclade process will allow the pipeline to finish with errors:

errorStrategy 'ignore'