Error creating report in Kraken

[rachelhawrit]

Operating System

macOS

Other Linux

No response

Workflow Version

v1.1.3

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v1.1.3

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

It appears to only make tax abundance table for barcode 22. However, barcode 22 should not even have reads as we only used 16 for this run. I was wanting to get a taxa barplot output. My parameters are listed in the log

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/main.nf` [frosty_stallman] DSL2 - revision: 8363748886
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
WARN: Found unexpected parameters:
* --client_fields: /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/client_fields.json
- Ignore this warning: params.schema_ignore_params = "client_fields" 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-16s v1.1.3
--------------------------------------------------------------------------------
Core Nextflow options
  runName            : frosty_stallman
  containerEngine    : docker
  launchDir          : /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V
  workDir            : /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/work
  projectDir         : /Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s
  userName           : rachelritt
  profile            : standard
  configFiles        : /Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/nextflow.config
Input Options
  fastq              : /Users/rachelritt/Desktop/premier/binf3201_2024/james/fastq_pass
  classifier         : kraken2
Real Time Analysis Options
  real_time          : true
  batch_size         : 2000
  server_threads     : 5
  kraken_clients     : 3
Sample Options
  sample_sheet       : /Users/rachelritt/Desktop/premier/binf3201_2024/james.csv
Reference Options
  store_dir          : /Users/rachelritt/epi2melabs/data
  database_sets      : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null]]
Report Options
  abundance_threshold: 5
  n_taxa_barplot     : 20
Output Options
  out_dir            : /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/output
Advanced Options
  min_len            : 1000
  max_len            : 1800
  threads            : 6
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-16s for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-16s v1.1.3.
--------------------------------------------------------------------------------
Checking inputs.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis.
Kraken2 pipeline.
Preparing databases.
Using default taxonomy database.
Unpacking kraken2 indexes
The `sample_sheet` parameter is not used in the real time mode.
Workflow will run indefinitely as no read_limit is set.
Workflow will stop processing files after null reads.
[skipping] Stored process > prepare_databases:unpack_download_kraken2_database
[skipping] Stored process > prepare_databases:download_unpack_taxonomy
[skipping] Stored process > prepare_databases:determine_bracken_length
[2e/022d97] Submitted process > fastcat (6)
[08/b94f92] Submitted process > fastcat (5)
[b3/bd98e0] Submitted process > real_time_pipeline:run_common:getParams
[0d/2953d3] Submitted process > real_time_pipeline:run_common:getVersions
[9e/39d219] Submitted process > fastcat (1)
[f8/d83f21] Submitted process > real_time_pipeline:output_results (1)
[e2/84f284] Submitted process > fastcat (8)
[cb/7e2ce5] Submitted process > fastcat (3)
[9d/9cb0a4] Submitted process > fastcat (4)
[2d/9ff4b5] Submitted process > fastcat (7)
WARN: Found empty file for sample 'barcode19'.
[0c/74a165] Submitted process > fastcat (2)
[17/3769f1] Submitted process > real_time_pipeline:rebatchFastq (barcode21)
WARN: Found empty file for sample 'barcode20'.
[65/01c7c7] Submitted process > fastcat (9)
[06/bc78ee] Submitted process > real_time_pipeline:rebatchFastq (barcode21)
[76/c67444] Submitted process > fastcat (10)
[bd/8bad63] Submitted process > fastcat (11)
[5d/f47bcd] Submitted process > real_time_pipeline:rebatchFastq (barcode17)
[85/22e4eb] Submitted process > fastcat (12)
[d1/c6d238] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[52/710b85] Submitted process > fastcat (13)
[2f/baf329] Submitted process > real_time_pipeline:rebatchFastq (barcode10)
[7c/a7d70e] Submitted process > fastcat (15)
[2a/12bb16] Submitted process > fastcat (14)
[2f/1fdcec] Submitted process > real_time_pipeline:output_results (2)
[6c/fd680a] Submitted process > real_time_pipeline:kraken2_client (barcode21)
[db/ebe06f] Submitted process > fastcat (16)
[0c/43f50d] Submitted process > fastcat (17)
[43/de952b] Submitted process > real_time_pipeline:kraken2_client (barcode21)
[03/90f938] Submitted process > fastcat (18)
[26/573678] Submitted process > fastcat (19)
[bb/5cc647] Submitted process > fastcat (20)
[99/9f3365] Submitted process > fastcat (21)
[e6/ea6466] Submitted process > fastcat (27)
[71/d20413] Submitted process > fastcat (22)
[dd/4f0002] Submitted process > fastcat (23)
[df/f19703] Submitted process > fastcat (29)
[4e/00b2cf] Submitted process > fastcat (24)
[0f/fe3cd1] Submitted process > fastcat (25)
[15/89d6da] Submitted process > fastcat (26)
[e9/84b72a] Submitted process > fastcat (28)
[e3/2efc69] Submitted process > fastcat (30)
[37/727b60] Submitted process > fastcat (32)
[4b/8a4342] Submitted process > fastcat (31)
[cb/afd477] Submitted process > fastcat (34)
[78/0bc452] Submitted process > fastcat (33)
[54/23d184] Submitted process > fastcat (39)
[72/40fa30] Submitted process > fastcat (35)
[62/51e832] Submitted process > fastcat (42)
[68/2cc35f] Submitted process > fastcat (36)
[e8/b03782] Submitted process > fastcat (37)
[6b/d9df16] Submitted process > fastcat (43)
[cb/8e8251] Submitted process > fastcat (38)
[6e/9197cd] Submitted process > fastcat (47)
[dc/9e041e] Submitted process > fastcat (40)
[b1/d40df0] Submitted process > fastcat (41)
[37/7cdd69] Submitted process > fastcat (50)
[92/c44bfb] Submitted process > fastcat (44)
[0c/a73b43] Submitted process > fastcat (45)
[07/8d2364] Submitted process > fastcat (52)
[7b/ee53e5] Submitted process > fastcat (46)
[22/99545a] Submitted process > fastcat (48)
[15/fad680] Submitted process > fastcat (49)
[81/e9b604] Submitted process > fastcat (51)
[dc/0eff16] Submitted process > fastcat (58)
[7f/866101] Submitted process > fastcat (59)
[27/1d2828] Submitted process > fastcat (54)
[d3/cc197c] Submitted process > fastcat (55)
[14/a04a25] Submitted process > fastcat (60)
[c3/bd0685] Submitted process > fastcat (53)
[7d/9ff83c] Submitted process > fastcat (61)
[52/ec68b0] Submitted process > fastcat (64)
[96/846f7e] Submitted process > fastcat (65)
[16/18c116] Submitted process > fastcat (66)
[fa/17fe61] Submitted process > fastcat (68)
[2b/1a8e40] Submitted process > fastcat (56)
[30/d3cd92] Submitted process > fastcat (70)
[e6/a0bea1] Submitted process > fastcat (57)
[16/40c61e] Submitted process > fastcat (69)
[fa/0bf291] Submitted process > fastcat (72)
[05/c68087] Submitted process > fastcat (62)
[53/eef314] Submitted process > fastcat (75)
[a6/72aedd] Submitted process > fastcat (74)
[39/85b1c2] Submitted process > fastcat (63)
[db/1691e5] Submitted process > fastcat (76)
[d3/2621b6] Submitted process > fastcat (67)
[23/455373] Submitted process > fastcat (78)
[65/055a77] Submitted process > fastcat (80)
[9e/9ec9f4] Submitted process > fastcat (71)
[77/678246] Submitted process > fastcat (83)
[af/1513c3] Submitted process > fastcat (84)
[7a/8fff30] Submitted process > fastcat (85)
[36/af9256] Submitted process > fastcat (73)
[fe/9dc486] Submitted process > fastcat (77)
[71/83a9c4] Submitted process > fastcat (79)
[50/fac802] Submitted process > fastcat (81)
[8c/150ea4] Submitted process > fastcat (82)
[1e/9139b1] Submitted process > fastcat (92)
[f4/b0a638] Submitted process > fastcat (91)
[f7/811cef] Submitted process > fastcat (86)
[45/b9fffe] Submitted process > fastcat (88)
[08/9fd575] Submitted process > fastcat (94)
[10/23931a] Submitted process > fastcat (87)
[96/e303ea] Submitted process > fastcat (89)
[66/c94af1] Submitted process > fastcat (97)
[ab/7c0ae2] Submitted process > fastcat (90)
[18/166a1a] Submitted process > fastcat (99)
[81/000a9d] Submitted process > fastcat (93)
[7b/08c915] Submitted process > fastcat (102)
WARN: Found empty file for sample 'barcode22'.
[1c/da23a4] Submitted process > fastcat (95)
[b1/10445f] Submitted process > fastcat (96)
[ee/d849d1] Submitted process > fastcat (98)
[bb/b4ce18] Submitted process > fastcat (100)
[eb/e19a30] Submitted process > fastcat (107)
[5c/bbb480] Submitted process > fastcat (101)
WARN: Found empty file for sample 'barcode15'.
[fd/1974b6] Submitted process > fastcat (103)
WARN: Found empty file for sample 'barcode22'.
[1f/698315] Submitted process > fastcat (104)
[86/d47b46] Submitted process > fastcat (106)
WARN: Found empty file for sample 'barcode24'.
[f7/3b9d29] Submitted process > fastcat (105)
WARN: Found empty file for sample 'barcode23'.
[58/b492de] Submitted process > fastcat (113)
WARN: Found empty file for sample 'barcode24'.
[52/6697c5] Submitted process > fastcat (108)
[c0/362846] Submitted process > fastcat (114)
[ca/1d6dc6] Submitted process > fastcat (109)
[a7/e8aa0f] Submitted process > fastcat (110)
[3d/1313bf] Submitted process > fastcat (111)
[8d/25cd93] Submitted process > fastcat (112)
[8f/9f1dc6] Submitted process > fastcat (117)
[7d/02ddce] Submitted process > fastcat (119)
[ef/d28982] Submitted process > fastcat (115)
[d5/7121d8] Submitted process > fastcat (121)
[f2/294928] Submitted process > fastcat (122)
[02/007db7] Submitted process > fastcat (120)
[29/1bc14f] Submitted process > fastcat (116)
[1b/efcce3] Submitted process > fastcat (118)
[ec/563c12] Submitted process > fastcat (126)
[55/51acb9] Submitted process > fastcat (127)
[53/e4d9c5] Submitted process > fastcat (125)
[6e/994429] Submitted process > fastcat (123)
[5b/3ecc8e] Submitted process > fastcat (124)
[99/0bd11e] Submitted process > fastcat (132)
[d9/18095d] Submitted process > fastcat (128)
[b4/e0df69] Submitted process > fastcat (133)
[98/4e0abf] Submitted process > fastcat (130)
[c9/ead896] Submitted process > fastcat (135)
[51/c25ebc] Submitted process > fastcat (136)
[d5/d55a4b] Submitted process > fastcat (138)
[ea/fef24b] Submitted process > fastcat (129)
[fd/0ea421] Submitted process > fastcat (131)
[9c/949de4] Submitted process > fastcat (142)
[40/04f8ee] Submitted process > fastcat (134)
[4f/c5a2ef] Submitted process > fastcat (144)
[6d/406c04] Submitted process > fastcat (137)
[c0/311dad] Submitted process > fastcat (148)
[37/78b115] Submitted process > fastcat (139)
[4e/ce4ce1] Submitted process > fastcat (145)
[e5/54cd6e] Submitted process > fastcat (141)
[4b/11f4b2] Submitted process > fastcat (146)
[81/07e8d1] Submitted process > fastcat (150)
[de/3ad0cd] Submitted process > fastcat (149)
[20/d8db28] Submitted process > fastcat (151)
[61/d7936e] Submitted process > fastcat (140)
[47/401a93] Submitted process > fastcat (153)
[8f/524865] Submitted process > fastcat (154)
[b0/55c868] Submitted process > fastcat (143)
[62/c57662] Submitted process > fastcat (155)
[ab/a817c1] Submitted process > fastcat (147)
[dd/591ecd] Submitted process > fastcat (158)
[a3/8814d5] Submitted process > fastcat (152)
[10/1345a1] Submitted process > fastcat (156)
[59/ce2919] Submitted process > fastcat (162)
[99/a53494] Submitted process > fastcat (163)
[3e/a50d0c] Submitted process > fastcat (160)
[7e/e13dbb] Submitted process > fastcat (164)
[3f/51f3f4] Submitted process > fastcat (161)
[c7/81dd69] Submitted process > fastcat (159)
[82/e44a0f] Submitted process > fastcat (167)
[45/65949f] Submitted process > fastcat (157)
[fa/881f1b] Submitted process > fastcat (165)
[22/95e607] Submitted process > fastcat (166)
[c9/7f2254] Submitted process > real_time_pipeline:rebatchFastq (barcode10)
[8d/45e687] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[c3/a3840a] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[96/602bcc] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[de/b481c6] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[91/33f2e6] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[ec/fca5b7] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[09/3c8586] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[d1/db7320] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[52/82bc55] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[db/2e4dd9] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[62/374ce4] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[b3/8ab8fe] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[2e/3a556b] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[f4/2b06aa] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[30/9fb604] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[f3/ee6546] Submitted process > real_time_pipeline:rebatchFastq (barcode11)
[4d/073d1d] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[e6/1b1a6a] Submitted process > real_time_pipeline:rebatchFastq (barcode16)
[e0/652c05] Submitted process > real_time_pipeline:rebatchFastq (barcode16)
[74/1de5de] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[4e/ad9e39] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[97/a10e83] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[e8/2bf60e] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[ed/731a1d] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[90/9f8cd0] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[53/049085] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[df/2bef1b] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[a7/3c15f1] Submitted process > real_time_pipeline:rebatchFastq (barcode02)
[64/bbd82a] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[9e/3de197] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[25/36982f] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[96/32892d] Submitted process > real_time_pipeline:rebatchFastq (barcode02)
[f3/d2cdf7] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[d7/b919ff] Submitted process > real_time_pipeline:rebatchFastq (barcode05)
[39/1864a3] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[65/63f621] Submitted process > real_time_pipeline:rebatchFastq (barcode02)
[df/a956ca] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[55/f6fd84] Submitted process > real_time_pipeline:rebatchFastq (barcode02)
[7c/980752] Submitted process > real_time_pipeline:rebatchFastq (barcode02)
[74/1a5f65] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[86/8dc9ef] Submitted process > real_time_pipeline:rebatchFastq (barcode02)
[f5/2cad1b] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[a6/c2170b] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[60/1425c6] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[e2/30fee5] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[2c/aab258] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[86/9a469b] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[2c/cb6b66] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[b0/fec31c] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[fa/769dd7] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[45/06fd91] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[34/55ff41] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[dd/46ccdb] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[c0/a87dcd] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[5e/3106c0] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[f3/364df3] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[dd/c0c50e] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[0c/3579df] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[e0/bdf236] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[3c/f85ea3] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[11/aa06a6] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[a6/07d6e0] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[37/78d9b3] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[d5/7c0249] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[85/f7a68e] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[39/1734c1] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[03/8a5ee4] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[ac/a85d2f] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[59/96809d] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[f2/ec71ea] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[9b/60b927] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[fb/4fa2b2] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[86/cd86b6] Submitted process > real_time_pipeline:rebatchFastq (barcode03)
[66/4768e0] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[07/1dffd9] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[1e/6b43c0] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[af/e99822] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[65/4516f6] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[73/9ccd43] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[ad/3e41af] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[80/99542e] Submitted process > real_time_pipeline:rebatchFastq (barcode04)
[7a/fcf003] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[40/b1d053] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[49/a7c0f0] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[13/f3ba70] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[8d/778bf3] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[9f/d2cd02] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[a2/9a7709] Submitted process > real_time_pipeline:rebatchFastq (barcode13)
[23/8aaeb2] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[db/bd95dd] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[99/f6c004] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[f8/cf932a] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[4b/020042] Submitted process > real_time_pipeline:rebatchFastq (barcode14)
[8a/f8f18e] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[26/e82d74] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[83/7b9923] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[04/664b25] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[b8/285d45] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[d4/2c83c9] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[4f/2199e3] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[64/5b7ccf] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[2d/089d06] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[52/061d44] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[b6/558aa1] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[d8/36b102] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[29/e99911] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[0e/692e07] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[12/cf914c] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[be/66217c] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[38/eb3908] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[79/54f653] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[ea/927ab9] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[ed/030406] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[e5/14fd6d] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[43/3a8121] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[47/dfe4f6] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[28/ce08bd] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[b7/42f7d6] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[c7/e02662] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[e5/f927d8] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[72/1b8fc7] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[48/405f08] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[31/9a92ec] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[5d/6677de] Submitted process > real_time_pipeline:rebatchFastq (barcode12)
[4b/b602d4] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[f9/972b5d] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[5e/7fce3c] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[c7/2b8611] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[58/2f17ca] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[d5/e7e8e0] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[ab/9c938e] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[23/0a9095] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[10/3212c7] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[ee/ad07c2] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[3d/a160be] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[e3/c19eb6] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[39/d0245b] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[cc/37c561] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[9a/2945e9] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[45/e0eb22] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[c6/b234b1] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[5c/827792] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[77/8c374a] Submitted process > real_time_pipeline:rebatchFastq (barcode06)
[0a/d2396b] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[4c/f7a329] Submitted process > real_time_pipeline:rebatchFastq (barcode01)
[0e/e6352d] Submitted process > real_time_pipeline:rebatchFastq (barcode06)
[e7/cbfc9e] Submitted process > real_time_pipeline:rebatchFastq (barcode07)
[0a/e8a450] Submitted process > real_time_pipeline:rebatchFastq (barcode06)
[25/d07ba4] Submitted process > real_time_pipeline:rebatchFastq (barcode01)
[0d/250054] Submitted process > real_time_pipeline:rebatchFastq (barcode09)
[f7/e9187f] Submitted process > real_time_pipeline:rebatchFastq (barcode07)
[b4/b3ce71] Submitted process > real_time_pipeline:rebatchFastq (barcode08)
[de/6273f8] Submitted process > real_time_pipeline:rebatchFastq (barcode09)
[8f/f45e02] Submitted process > real_time_pipeline:kraken_server
[2f/b2e7a7] Submitted process > real_time_pipeline:kraken2_client (barcode17)
[eb/d1c626] Submitted process > real_time_pipeline:progressive_stats (1)
[da/773c3a] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[97/e29823] Submitted process > real_time_pipeline:kraken2_client (barcode10)
[34/a7a5ff] Submitted process > real_time_pipeline:progressive_kraken_reports (barcode21)
[a4/9fdde6] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[13/840060] Submitted process > real_time_pipeline:kraken2_client (barcode10)
[d8/adb895] Submitted process > real_time_pipeline:progressive_stats (2)
[bc/4c9f81] Submitted process > real_time_pipeline:kraken2_client (barcode10)
[3d/a17416] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[78/930072] Submitted process > real_time_pipeline:progressive_kraken_reports (barcode17)
[c4/69e2a8] Submitted process > real_time_pipeline:progressive_bracken (barcode21)
[36/ab16d5] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[ab/28b142] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[ee/2cc0d3] Submitted process > real_time_pipeline:progressive_stats (3)
ERROR ~ Error executing process > 'real_time_pipeline:progressive_bracken (barcode21)'
Caused by:
  Process `real_time_pipeline:progressive_bracken (barcode21)` terminated with an error exit status (255)
Command executed:
  # run bracken on the latest kreports, is this writing some outputs
  # alongside the inputs? seems at least {}.kreport_bracken_species.txt
  # is written alongside the input
  BRACKEN_LENGTH=$(cat "ncbi_targeted_loci_kraken2_db.bracken_length.txt")
  workflow-glue run_bracken         "ncbi_targeted_loci_kraken2_db"         "kraken.1.barcode21/barcode21.kreport.txt"         $BRACKEN_LENGTH         "G"         "barcode21.bracken_report.txt"

  # do some stuff...
  awk -F '  ' -v OFS='  ' '{ print $2,$6 }' "barcode21.bracken_report.txt"         | awk -F '   ' -v OFS='  ' 'NR!=1 {print}'         | tee taxacounts.txt         | awk -F '   ' -v OFS='  ' '{ print $1 }' > taxa.txt
  taxonkit lineage         -j 1         --data-dir taxdmp_2023-01-01_db         -R taxa.txt  > lineages.txt
  workflow-glue aggregate_lineages_bracken         -i "lineages.txt" -b "taxacounts.txt"         -u "kraken.1.barcode21/barcode21.kreport.txt"         -p "barcode21.kraken2"         -r "G" 
  file1=$(find -name '*.json' -exec cat {} +)
  echo "{"'"barcode21"'": $file1}" >> "bracken.json"

  # collate the latest bracken outputs into state
  if [[ "1" != "1" ]]; then
      cp -r "NOSTATE" "bracken.1"
  else
      # make fresh directory
      mkdir "bracken.1"
  fi;

  # first output here is just for end user
  mv "kraken.1.barcode21/barcode21.kreport_bracken_species.txt" "bracken.1" || echo "No bracken report"
  mv "bracken.json" "bracken.1/barcode21.json"
Command exit status:
  255
Command output:
  b' >> Checking for Valid Options...\n >> Running Bracken \n      >> python src/est_abundance.py -i kraken.1.barcode21/barcode21.kreport.txt -o barcode21.bracken_report.txt -k ncbi_targeted_loci_kraken2_db/database1000mers.kmer_distrib -l G -t 0\nPROGRAM START TIME: 05-14-2024 23:58:12\nBRACKEN SUMMARY (Kraken report: kraken.1.barcode21/barcode21.kreport.txt)\n    >>> Threshold: 0 \n    >>> Number of genuses in sample: 1 \n\t  >> Number of genuses with reads > threshold: 1 \n\t  >> Number of genuses with reads < threshold: 0 \n    >>> Total reads in sample: 1\n\t  >> Total reads kept at genuses level (reads > threshold): 1\n\t  >> Total reads discarded (genuses reads < threshold): 0\n\t  >> Reads distributed: 0\n\t  >> Reads not distributed (eg. no genuses above threshold): 0\n\t  >> Unclassified reads: 0\nBRACKEN OUTPUT PRODUCED: barcode21.bracken_report.txt\nPROGRAM END TIME: 05-14-2024 23:58:12\n  Bracken complete.\n'
Command error:
  [23:58:11 - matplotlib.font_manager] generated new fontManager
  [23:58:12 - workflow_glue] Starting entrypoint.
  b'>> Checking report file: kraken.1.barcode21/barcode21.kreport.txt\n'b' >> Checking for Valid Options...\n >> Running Bracken \n      >> python src/est_abundance.py -i kraken.1.barcode21/barcode21.kreport.txt -o barcode21.bracken_report.txt -k ncbi_targeted_loci_kraken2_db/database1000mers.kmer_distrib -l G -t 0\nPROGRAM START TIME: 05-14-2024 23:58:12\nBRACKEN SUMMARY (Kraken report: kraken.1.barcode21/barcode21.kreport.txt)\n    >>> Threshold: 0 \n    >>> Number of genuses in sample: 1 \n\t  >> Number of genuses with reads > threshold: 1 \n\t  >> Number of genuses with reads < threshold: 0 \n    >>> Total reads in sample: 1\n\t  >> Total reads kept at genuses level (reads > threshold): 1\n\t  >> Total reads discarded (genuses reads < threshold): 0\n\t  >> Reads distributed: 0\n\t  >> Reads not distributed (eg. no genuses above threshold): 0\n\t  >> Unclassified reads: 0\nBRACKEN OUTPUT PRODUCED: barcode21.bracken_report.txt\nPROGRAM END TIME: 05-14-2024 23:58:12\n  Bracken complete.\n'23:58:13.461 [ERRO] taxonomy data not found, please download and uncompress ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz, and copy "names.dmp", "nodes.dmp", "delnodes.dmp", and "merged.dmp" to taxdmp_2023-01-01_db
Work dir:
  /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/work/c4/69e2a87b01ce7eeb0cf802e08b38e8
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
 -- Check '/Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/nextflow.log' file for details
WARN: Killing running tasks (2)
N E X T F L O W  ~  version 23.04.2
Launching `/Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/main.nf` [floored_dijkstra] DSL2 - revision: 8363748886
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
WARN: Found unexpected parameters:
* --client_fields: /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/client_fields.json
- Ignore this warning: params.schema_ignore_params = "client_fields" 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-16s v1.1.3
--------------------------------------------------------------------------------
Core Nextflow options
  runName            : floored_dijkstra
  containerEngine    : docker
  launchDir          : /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V
  workDir            : /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/work
  projectDir         : /Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s
  userName           : rachelritt
  profile            : standard
  configFiles        : /Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/nextflow.config
Input Options
  fastq              : /Users/rachelritt/Desktop/premier/binf3201_2024/james/fastq_pass
  classifier         : kraken2
Real Time Analysis Options
  real_time          : true
  batch_size         : 2000
  server_threads     : 5
  kraken_clients     : 3
Sample Options
  sample_sheet       : /Users/rachelritt/Desktop/premier/binf3201_2024/james.csv
Reference Options
  store_dir          : /Users/rachelritt/epi2melabs/data
  database_sets      : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null]]
Report Options
  abundance_threshold: 5
  n_taxa_barplot     : 20
Output Options
  out_dir            : /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/output
Advanced Options
  min_len            : 1000
  max_len            : 1800
  threads            : 6
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-16s for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-16s v1.1.3.
--------------------------------------------------------------------------------
Checking inputs.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis.
Kraken2 pipeline.
Preparing databases.
Using default taxonomy database.
Unpacking kraken2 indexes
The `sample_sheet` parameter is not used in the real time mode.
Workflow will run indefinitely as no read_limit is set.
Workflow will stop processing files after null reads.
[skipping] Stored process > prepare_databases:download_unpack_taxonomy
[skipping] Stored process > prepare_databases:unpack_download_kraken2_database
[skipping] Stored process > prepare_databases:determine_bracken_length
[0d/2953d3] Cached process > real_time_pipeline:run_common:getVersions
[e2/84f284] Cached process > fastcat (8)
[08/b94f92] Cached process > fastcat (5)
[cb/7e2ce5] Cached process > fastcat (3)
[2e/022d97] Cached process > fastcat (6)
[9d/9cb0a4] Cached process > fastcat (4)
[9e/39d219] Cached process > fastcat (1)
[b3/bd98e0] Cached process > real_time_pipeline:run_common:getParams
[0c/74a165] Cached process > fastcat (2)
[2d/9ff4b5] Cached process > fastcat (7)
[65/01c7c7] Cached process > fastcat (9)
[f8/d83f21] Cached process > real_time_pipeline:output_results (1)
[bd/8bad63] Cached process > fastcat (11)
[76/c67444] Cached process > fastcat (10)
[85/22e4eb] Cached process > fastcat (12)
[2f/1fdcec] Cached process > real_time_pipeline:output_results (2)
[52/710b85] Cached process > fastcat (13)
[26/573678] Cached process > fastcat (19)
[7c/a7d70e] Cached process > fastcat (15)
[0c/43f50d] Cached process > fastcat (17)
[03/90f938] Cached process > fastcat (18)
[2a/12bb16] Cached process > fastcat (14)
[db/ebe06f] Cached process > fastcat (16)
WARN: Found empty file for sample 'barcode19'.
WARN: Found empty file for sample 'barcode20'.
[bb/5cc647] Cached process > fastcat (20)
[99/9f3365] Cached process > fastcat (21)
[71/d20413] Cached process > fastcat (22)
[e6/ea6466] Cached process > fastcat (27)
[4e/00b2cf] Cached process > fastcat (24)
[e9/84b72a] Cached process > fastcat (28)
[dd/4f0002] Cached process > fastcat (23)
[e3/2efc69] Cached process > fastcat (30)
[15/89d6da] Cached process > fastcat (26)
[df/f19703] Cached process > fastcat (29)
[06/bc78ee] Cached process > real_time_pipeline:rebatchFastq (barcode21)
[17/3769f1] Cached process > real_time_pipeline:rebatchFastq (barcode21)
[e2/2d9fc3] Submitted process > real_time_pipeline:kraken_server
[5d/f47bcd] Cached process > real_time_pipeline:rebatchFastq (barcode17)
[8d/45e687] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[c9/7f2254] Cached process > real_time_pipeline:rebatchFastq (barcode10)
[d1/c6d238] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[37/727b60] Cached process > fastcat (32)
[96/602bcc] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[2f/baf329] Cached process > real_time_pipeline:rebatchFastq (barcode10)
[4b/8a4342] Cached process > fastcat (31)
[78/0bc452] Cached process > fastcat (33)
[0f/fe3cd1] Cached process > fastcat (25)
[c3/a3840a] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[cb/afd477] Cached process > fastcat (34)
[de/b481c6] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[68/2cc35f] Cached process > fastcat (36)
[72/40fa30] Cached process > fastcat (35)
[e8/b03782] Cached process > fastcat (37)
[91/33f2e6] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[cb/8e8251] Cached process > fastcat (38)
[2e/3a556b] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[d1/db7320] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[b3/8ab8fe] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[09/3c8586] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[30/9fb604] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[54/23d184] Cached process > fastcat (39)
[52/82bc55] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[b1/d40df0] Cached process > fastcat (41)
[dc/9e041e] Cached process > fastcat (40)
[ec/fca5b7] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[db/2e4dd9] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[6b/d9df16] Cached process > fastcat (43)
[62/51e832] Cached process > fastcat (42)
[62/374ce4] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[f3/ee6546] Cached process > real_time_pipeline:rebatchFastq (barcode11)
[92/c44bfb] Cached process > fastcat (44)
[0c/a73b43] Cached process > fastcat (45)
[7b/ee53e5] Cached process > fastcat (46)
[6e/9197cd] Cached process > fastcat (47)
[15/fad680] Cached process > fastcat (49)
[22/99545a] Cached process > fastcat (48)
[37/7cdd69] Cached process > fastcat (50)
[4e/ad9e39] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[81/e9b604] Cached process > fastcat (51)
[07/8d2364] Cached process > fastcat (52)
[97/a10e83] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[f4/2b06aa] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[4d/073d1d] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[e6/1b1a6a] Cached process > real_time_pipeline:rebatchFastq (barcode16)
[e8/2bf60e] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[27/1d2828] Cached process > fastcat (54)
[d3/cc197c] Cached process > fastcat (55)
[c3/bd0685] Cached process > fastcat (53)
[2b/1a8e40] Cached process > fastcat (56)
[e6/a0bea1] Cached process > fastcat (57)
[ed/731a1d] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[dc/0eff16] Cached process > fastcat (58)
[7f/866101] Cached process > fastcat (59)
[14/a04a25] Cached process > fastcat (60)
[e0/652c05] Cached process > real_time_pipeline:rebatchFastq (barcode16)
[64/bbd82a] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[53/049085] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[74/1de5de] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[05/c68087] Cached process > fastcat (62)
[df/2bef1b] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[39/85b1c2] Cached process > fastcat (63)
[52/ec68b0] Cached process > fastcat (64)
[7d/9ff83c] Cached process > fastcat (61)
[96/846f7e] Cached process > fastcat (65)
[f3/d2cdf7] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[90/9f8cd0] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[96/32892d] Cached process > real_time_pipeline:rebatchFastq (barcode02)
[55/f6fd84] Cached process > real_time_pipeline:rebatchFastq (barcode02)
[16/18c116] Cached process > fastcat (66)
[fa/17fe61] Cached process > fastcat (68)
[d7/b919ff] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[30/d3cd92] Cached process > fastcat (70)
[16/40c61e] Cached process > fastcat (69)
[36/af9256] Cached process > fastcat (73)
[fa/0bf291] Cached process > fastcat (72)
[d3/2621b6] Cached process > fastcat (67)
[9e/9ec9f4] Cached process > fastcat (71)
[a6/72aedd] Cached process > fastcat (74)
[7c/980752] Cached process > real_time_pipeline:rebatchFastq (barcode02)
[6c/fd680a] Cached process > real_time_pipeline:kraken2_client (barcode21)
[8c/150ea4] Cached process > fastcat (82)
[50/fac802] Cached process > fastcat (81)
[65/055a77] Cached process > fastcat (80)
[53/eef314] Cached process > fastcat (75)
[25/36982f] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[77/678246] Cached process > fastcat (83)
[af/1513c3] Cached process > fastcat (84)
[60/1425c6] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[db/1691e5] Cached process > fastcat (76)
[65/63f621] Cached process > real_time_pipeline:rebatchFastq (barcode02)
[71/83a9c4] Cached process > fastcat (79)
[10/23931a] Cached process > fastcat (87)
[86/8dc9ef] Cached process > real_time_pipeline:rebatchFastq (barcode02)
[df/a956ca] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[f4/b0a638] Cached process > fastcat (91)
[f3/0523f8] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[1e/9139b1] Cached process > fastcat (92)
[81/000a9d] Cached process > fastcat (93)
[e2/30fee5] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[7a/8fff30] Cached process > fastcat (85)
[86/9a469b] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[f3/364df3] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[36/59bb9b] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[08/9fd575] Cached process > fastcat (94)
[f7/811cef] Cached process > fastcat (86)
[ab/7c0ae2] Cached process > fastcat (90)
[96/e303ea] Cached process > fastcat (89)
[1c/da23a4] Cached process > fastcat (95)
[45/b9fffe] Cached process > fastcat (88)
[f5/2cad1b] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[66/c94af1] Cached process > fastcat (97)
[2c/aab258] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[bb/b4ce18] Cached process > fastcat (100)
[b0/fec31c] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[b1/10445f] Cached process > fastcat (96)
[18/166a1a] Cached process > fastcat (99)
[fd/1974b6] Cached process > fastcat (103)
[5c/bbb480] Cached process > fastcat (101)
[d5/7c0249] Cached process > real_time_pipeline:rebatchFastq (barcode03)
WARN: Found empty file for sample 'barcode22'.
[fe/9dc486] Cached process > fastcat (77)
[74/1a5f65] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[23/455373] Cached process > fastcat (78)
[7b/08c915] Cached process > fastcat (102)
[0c/3579df] Cached process > real_time_pipeline:rebatchFastq (barcode03)
WARN: Found empty file for sample 'barcode22'.
[ca/1d6dc6] Cached process > fastcat (109)
[a7/e8aa0f] Cached process > fastcat (110)
[eb/e19a30] Cached process > fastcat (107)
[52/6697c5] Cached process > fastcat (108)
[3d/1313bf] Cached process > fastcat (111)
[a7/3c15f1] Cached process > real_time_pipeline:rebatchFastq (barcode02)
[f7/3b9d29] Cached process > fastcat (105)
[1f/698315] Cached process > fastcat (104)
[34/55ff41] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[9e/3de197] Cached process > real_time_pipeline:rebatchFastq (barcode05)
[86/d47b46] Cached process > fastcat (106)
[a4/7425d9] Submitted process > real_time_pipeline:progressive_kraken_reports (barcode21)
[8d/25cd93] Cached process > fastcat (112)
WARN: Found empty file for sample 'barcode15'.
[ee/d849d1] Cached process > fastcat (98)
[58/b492de] Cached process > fastcat (113)
[45/06fd91] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[8f/9f1dc6] Cached process > fastcat (117)
[5e/3106c0] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[7d/02ddce] Cached process > fastcat (119)
WARN: Found empty file for sample 'barcode24'.
WARN: Found empty file for sample 'barcode23'.
[a6/c2170b] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[29/1bc14f] Cached process > fastcat (116)
[ef/d28982] Cached process > fastcat (115)
[1b/efcce3] Cached process > fastcat (118)
[11/aa06a6] Cached process > real_time_pipeline:rebatchFastq (barcode03)
WARN: Found empty file for sample 'barcode24'.
[3c/f85ea3] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[f2/294928] Cached process > fastcat (122)
[02/007db7] Cached process > fastcat (120)
[5b/3ecc8e] Cached process > fastcat (124)
[53/e4d9c5] Cached process > fastcat (125)
[dd/46ccdb] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[d9/18095d] Cached process > fastcat (128)
[d5/7121d8] Cached process > fastcat (121)
[59/96809d] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[39/1864a3] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[e0/bdf236] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[c0/362846] Cached process > fastcat (114)
[c0/a87dcd] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[86/cd86b6] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[6e/994429] Cached process > fastcat (123)
[2c/cb6b66] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[55/51acb9] Cached process > fastcat (127)
[ea/fef24b] Cached process > fastcat (129)
[fd/0ea421] Cached process > fastcat (131)
[98/4e0abf] Cached process > fastcat (130)
[ec/563c12] Cached process > fastcat (126)
[a6/07d6e0] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[99/0bd11e] Cached process > fastcat (132)
[fa/769dd7] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[dd/c0c50e] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[c9/ead896] Cached process > fastcat (135)
[51/c25ebc] Cached process > fastcat (136)
[40/04f8ee] Cached process > fastcat (134)
[b4/e0df69] Cached process > fastcat (133)
[6d/406c04] Cached process > fastcat (137)
[03/8a5ee4] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[f2/ec71ea] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[d5/d55a4b] Cached process > fastcat (138)
[e5/54cd6e] Cached process > fastcat (141)
[07/1dffd9] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[37/78d9b3] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[9c/949de4] Cached process > fastcat (142)
[40/b1d053] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[9b/60b927] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[85/f7a68e] Cached process > real_time_pipeline:rebatchFastq (barcode03)
[61/d7936e] Cached process > fastcat (140)
[af/e99822] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[4e/ce4ce1] Cached process > fastcat (145)
[a2/9a7709] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[4b/11f4b2] Cached process > fastcat (146)
[4f/c5a2ef] Cached process > fastcat (144)
[c0/311dad] Cached process > fastcat (148)
[de/3ad0cd] Cached process > fastcat (149)
[ab/a817c1] Cached process > fastcat (147)
[a3/8814d5] Cached process > fastcat (152)
[b0/55c868] Cached process > fastcat (143)
[fb/4fa2b2] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[20/d8db28] Cached process > fastcat (151)
[37/78b115] Cached process > fastcat (139)
[ac/a85d2f] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[1e/6b43c0] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[47/401a93] Cached process > fastcat (153)
[81/07e8d1] Cached process > fastcat (150)
[73/9ccd43] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[65/4516f6] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[8f/524865] Cached process > fastcat (154)
[45/65949f] Cached process > fastcat (157)
[62/c57662] Cached process > fastcat (155)
[10/1345a1] Cached process > fastcat (156)
[dd/591ecd] Cached process > fastcat (158)
[3e/a50d0c] Cached process > fastcat (160)
[3f/51f3f4] Cached process > fastcat (161)
[c7/81dd69] Cached process > fastcat (159)
[99/a53494] Cached process > fastcat (163)
[59/ce2919] Cached process > fastcat (162)
[82/e44a0f] Cached process > fastcat (167)
[22/95e607] Cached process > fastcat (166)
[fa/881f1b] Cached process > fastcat (165)
[7e/e13dbb] Cached process > fastcat (164)
[7a/fcf003] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[23/8aaeb2] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[49/a7c0f0] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[80/99542e] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[8d/778bf3] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[13/f3ba70] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[db/bd95dd] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[f8/cf932a] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[9f/d2cd02] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[4b/020042] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[39/1734c1] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[04/664b25] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[b8/285d45] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[26/e82d74] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[4f/2199e3] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[99/f6c004] Cached process > real_time_pipeline:rebatchFastq (barcode14)
[ad/3e41af] Cached process > real_time_pipeline:rebatchFastq (barcode13)
[8a/f8f18e] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[d4/2c83c9] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[12/cf914c] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[52/061d44] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[0e/692e07] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[2d/089d06] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[64/5b7ccf] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[ed/030406] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[d8/36b102] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[ea/927ab9] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[48/405f08] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[38/eb3908] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[72/1b8fc7] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[be/66217c] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[28/ce08bd] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[83/7b9923] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[43/3a8121] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[b6/558aa1] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[f9/972b5d] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[e5/14fd6d] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[e5/f927d8] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[58/2f17ca] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[66/4768e0] Cached process > real_time_pipeline:rebatchFastq (barcode04)
[29/e99911] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[5d/6677de] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[4b/b602d4] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[10/3212c7] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[5e/7fce3c] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[c7/e02662] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[23/0a9095] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[45/e0eb22] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[b7/42f7d6] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[e3/c19eb6] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[c7/2b8611] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[ee/ad07c2] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[5c/827792] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[cc/37c561] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[b4/b3ce71] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[c6/b234b1] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[4c/f7a329] Cached process > real_time_pipeline:rebatchFastq (barcode01)
[79/54f653] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[47/dfe4f6] Cached process > real_time_pipeline:rebatchFastq (barcode12)
[0a/e8a450] Cached process > real_time_pipeline:rebatchFastq (barcode06)
[25/d07ba4] Cached process > real_time_pipeline:rebatchFastq (barcode01)
[0e/e6352d] Cached process > real_time_pipeline:rebatchFastq (barcode06)
[3d/a160be] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[9a/2945e9] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[39/d0245b] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[de/6273f8] Cached process > real_time_pipeline:rebatchFastq (barcode09)
[f7/e9187f] Cached process > real_time_pipeline:rebatchFastq (barcode07)
[77/8c374a] Cached process > real_time_pipeline:rebatchFastq (barcode06)
[e7/cbfc9e] Cached process > real_time_pipeline:rebatchFastq (barcode07)
[31/9a92ec] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[0d/250054] Cached process > real_time_pipeline:rebatchFastq (barcode09)
[d5/e7e8e0] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[0a/d2396b] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[ab/9c938e] Cached process > real_time_pipeline:rebatchFastq (barcode08)
[98/3ea064] Submitted process > real_time_pipeline:progressive_stats (1)
[95/c636cb] Submitted process > real_time_pipeline:kraken2_client (barcode21)
[18/84f886] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[3b/45170e] Submitted process > real_time_pipeline:progressive_bracken (barcode21)
[01/08c7a9] Submitted process > real_time_pipeline:kraken2_client (barcode10)
[eb/89903a] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[dc/20b4ef] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[7b/8a24da] Submitted process > real_time_pipeline:kraken2_client (barcode10)
[97/75085a] Submitted process > real_time_pipeline:progressive_kraken_reports (barcode11)
[52/9b0ea9] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[7e/680a40] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[49/b45a29] Submitted process > real_time_pipeline:progressive_stats (2)
[ce/a7ae89] Submitted process > real_time_pipeline:kraken2_client (barcode17)
[7c/f39002] Submitted process > real_time_pipeline:kraken2_client (barcode10)
[f3/992a6e] Submitted process > real_time_pipeline:createAbundanceTables (1)
[f3/ca539b] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[5e/032487] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[14/712a39] Submitted process > real_time_pipeline:progressive_bracken (barcode11)
[60/2e78c5] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[81/9c8ddb] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[f0/c56783] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[65/8fbad9] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[ce/e98a4a] Submitted process > real_time_pipeline:progressive_kraken_reports (barcode11)
[16/2ce54b] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[46/47ce9d] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[83/01a121] Submitted process > real_time_pipeline:progressive_stats (3)
[87/ec5c19] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[a8/029900] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[3c/0dd891] Submitted process > real_time_pipeline:output_results (3)
[aa/59281c] Submitted process > real_time_pipeline:makeReport (1)
[19/0f2612] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[e6/8d13ac] Submitted process > real_time_pipeline:kraken2_client (barcode11)
[05/04842a] Submitted process > real_time_pipeline:createAbundanceTables (2)
ERROR ~ Error executing process > 'real_time_pipeline:makeReport (1)'
Caused by:
  Process `real_time_pipeline:makeReport (1)` terminated with an error exit status (1)
Command executed:
  workflow-glue report         "wf-16s-report.html"         --workflow_name wf-16s         --versions versions         --params params.json         --read_stats all_stats.1         --lineages "bracken.1"         --abundance_table "abundance_table_genus.tsv"         --taxonomic_rank "G"         --abundance_threshold "5"        --pipeline "real_time"         --n_taxa_barplot "20"
Command exit status:
  1
Command output:
  (empty)
Command error:
  [00:17:34 - workflow_glue] Could not load abundance_tables due to missing module anytree
  [00:17:42 - matplotlib.font_manager] generated new fontManager
  [00:17:43 - workflow_glue] Starting entrypoint.
  [00:17:43 - workflow_glue.Report    ] Sample barcode21.
  [00:17:43 - EChrtPlotr] Skipping axis label fixing
  [00:17:43 - workflow_glue.Report    ] Sample barcode11.
  [00:17:43 - EChrtPlotr] Skipping axis label fixing
  [00:17:43 - workflow_glue.Report    ] rank phylum.
  Traceback (most recent call last):
    File "/Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/bin/workflow-glue", line 7, in <module>
      cli()
    File "/Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/wf-metagenomics/bin/workflow_glue/__init__.py", line 72, in cli
      args.func(args)
    File "/Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/wf-metagenomics/bin/workflow_glue/report.py", line 213, in main
      most_abundant = report_utils.most_abundant_table(
    File "/Users/rachelritt/epi2melabs/workflows/epi2me-labs/wf-16s/wf-metagenomics/bin/workflow_glue/report_utils/report_utils.py", line 109, in most_abundant_table
      len(most_abundant_taxa['tax'].iloc[0].split(';'))-1)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 1073, in __getitem__
      return self._getitem_axis(maybe_callable, axis=axis)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 1625, in _getitem_axis
      self._validate_integer(key, axis)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/core/indexing.py", line 1557, in _validate_integer
      raise IndexError("single positional indexer is out-of-bounds")
  IndexError: single positional indexer is out-of-bounds
Work dir:
  /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/work/aa/59281c250ad015f4fc4e75317f52b2
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 -- Check '/Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/nextflow.log' file for details
WARN: Killing running tasks (4)

Application activity log entry

None are listed in red.

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

yes

Other demo data information

No response

[nggvs]

Hi @rachelhawrit ! Thanks for using the workflow! It seems that you have two different errors (as you have added two logs). When running real time, the option of providing a sample sheet is not possible. Could you share the content of /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/work/aa/59281c250ad015f4fc4e75317f52b2 /Users/rachelritt/epi2melabs/instances/wf-16s_01HXWRF0JCGBFGJ2SAF21R1W4V/work/c4/69e2a87b01ce7eeb0cf802e08b38e8 the sample_sheet?

Thank you very much in advance, Natalia

[nggvs]

Hi @rachelhawrit , are you still experiencing the same problem? If that is not the case would you mind to close the issue? Thank you very much in advance