Bacterial genome wf "Stopped with error"

[AnjaliSM22]

Operating System

Windows 11

Other Linux

No response

Workflow Version

v1.2.0

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?

Uploaded fastq files (92 files), it runs for about 30 mins and then shows a "stopped with error". Tried it a few times. I then troubleshooted with the demo-data and the workflow works. Opted to then run the files in batches of 10 and it works.

Relevant log output

N E X T F L O W ~ version 23.04.2
Launching `/mnt/c/Users/Sequencing/epi2melabs/workflows/epi2me-labs/wf-bacterial-genomes/main.nf` [competent_rosalind] DSL2 - revision: 67ff77f941
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-bacterial-genomes v1.2.0
--------------------------------------------------------------------------------
Core Nextflow options
runName : competent_rosalind
containerEngine: docker
launchDir : /mnt/c/Users/Sequencing/epi2melabs/instances/wf-bacterial-genomes_01JACZ50KNN6EF71EKC6551GPZ
workDir : /mnt/c/Users/Sequencing/epi2melabs/instances/wf-bacterial-genomes_01JACZ50KNN6EF71EKC6551GPZ/work
projectDir : /mnt/c/Users/Sequencing/epi2melabs/workflows/epi2me-labs/wf-bacterial-genomes
userName : epi2mewsl
profile : standard
configFiles : /mnt/c/Users/Sequencing/epi2melabs/workflows/epi2me-labs/wf-bacterial-genomes/nextflow.config
Input Options
fastq : /mnt/c/data/Anjali_colistin_16Oct2024/no_sample/20241016_1356_MN44856_FAZ04752_0602dabf/fastq_pass
Output Options
out_dir : /mnt/c/Users/Sequencing/epi2melabs/instances/wf-bacterial-genomes_01JACZ50KNN6EF71EKC6551GPZ/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-bacterial-genomes for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-bacterial-genomes v1.2.0.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Running Denovo assembly.
[47/7a7159] Submitted process > calling_pipeline:getParams
[5c/66f392] Submitted process > fastcat (2)
[19/fa4991] Submitted process > calling_pipeline:prokkaVersion
[14/4caee5] Submitted process > fastcat (1)
[e0/e89f79] Submitted process > fastcat (4)
[3b/f22c3d] Submitted process > fastcat (5)
[5b/a90141] Submitted process > fastcat (3)
[65/168365] Submitted process > fastcat (6)
[73/79fe56] Submitted process > calling_pipeline:lookup_medaka_consensus_model (1)
[1e/31f082] Submitted process > calling_pipeline:lookup_medaka_variant_model (1)
[ff/d1dcef] Submitted process > fastcat (7)
[b7/0c158b] Submitted process > fastcat (8)
[68/58af70] Submitted process > calling_pipeline:ingressCheckpoint (1)
[2a/e36ff6] Submitted process > fastcat (9)
[67/fb2c0f] Submitted process > fastcat (10)
[8d/06776a] Submitted process > fastcat (11)
[b9/28ca64] Submitted process > fastcat (12)
[28/4aadae] Submitted process > calling_pipeline:amrCheckpoint (1)
[27/bea04c] Submitted process > fastcat (13)
[b3/71e431] Submitted process > fastcat (14)
[69/878478] Submitted process > fastcat (15)
[15/36982e] Submitted process > fastcat (16)
[26/595280] Submitted process > calling_pipeline:variantCheckpoint (1)
[06/70d0da] Submitted process > fastcat (17)
[79/09e595] Submitted process > fastcat (18)
[7f/0ed4ef] Submitted process > fastcat (19)
[d1/3e946c] Submitted process > fastcat (20)
[3d/6085c3] Submitted process > calling_pipeline:perSampleReportingCheckpoint (1)
[8e/642502] Submitted process > fastcat (21)
[8a/36fd47] Submitted process > fastcat (22)
[a2/264c9f] Submitted process > fastcat (23)
[e8/c302db] Submitted process > calling_pipeline:perSampleReportingCheckpoint (2)
[6f/6534cb] Submitted process > fastcat (24)
[09/c152b1] Submitted process > fastcat (25)
[78/92ea46] Submitted process > calling_pipeline:ingressCheckpoint (2)
[8a/9b01d1] Submitted process > fastcat (26)
[95/7ea4f4] Submitted process > fastcat (27)
[f5/7e6e39] Submitted process > fastcat (28)
[68/44bb6f] Submitted process > calling_pipeline:amrCheckpoint (2)
[db/9afc43] Submitted process > fastcat (29)
[6a/9468b9] Submitted process > fastcat (30)
[08/628731] Submitted process > fastcat (31)
[3f/b019f2] Submitted process > fastcat (32)
[a6/bff595] Submitted process > calling_pipeline:medakaVersion
[68/d3d255] Submitted process > fastcat (33)
[98/c04318] Submitted process > calling_pipeline:variantCheckpoint (2)
[c2/f80915] Submitted process > fastcat (34)
[78/fd0edb] Submitted process > fastcat (35)
[2d/0b158a] Submitted process > fastcat (36)
[9c/635764] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (1)
[94/684993] Submitted process > fastcat (37)
[40/5e0d38] Submitted process > calling_pipeline:variantCheckpoint (3)
[86/7da59d] Submitted process > fastcat (38)
[25/ba0989] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (2)
[68/c51154] Submitted process > fastcat (39)
[a2/37e6a8] Submitted process > fastcat (40)
[27/81f971] Submitted process > fastcat (41)
[f5/417729] Submitted process > calling_pipeline:amrCheckpoint (3)
[93/c76c70] Submitted process > calling_pipeline:perSampleReportingCheckpoint (3)
[4f/2d46d0] Submitted process > calling_pipeline:ingressCheckpoint (3)
[ba/b8bbf2] Submitted process > fastcat (42)
[4a/9bffb4] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (3)
[5f/f83e85] Submitted process > fastcat (43)
[95/dbbbd7] Submitted process > calling_pipeline:ingressCheckpoint (4)
[4f/371b43] Submitted process > calling_pipeline:perSampleReportingCheckpoint (4)
[e9/066d59] Submitted process > calling_pipeline:amrCheckpoint (4)
[d0/a7f4e5] Submitted process > calling_pipeline:variantCheckpoint (4)
[55/d186c8] Submitted process > calling_pipeline:variantCheckpoint (5)
[d1/e9cb0b] Submitted process > calling_pipeline:amrCheckpoint (5)
[77/2ece43] Submitted process > calling_pipeline:ingressCheckpoint (5)
[f2/0a17d8] Submitted process > fastcat (44)
[c8/02461f] Submitted process > calling_pipeline:perSampleReportingCheckpoint (5)
[a6/65bef4] Submitted process > calling_pipeline:variantCheckpoint (6)
[18/dff1ba] Submitted process > calling_pipeline:amrCheckpoint (6)
[eb/c63ebf] Submitted process > calling_pipeline:perSampleReportingCheckpoint (6)
[7b/241d8a] Submitted process > calling_pipeline:ingressCheckpoint (6)
[18/5a008b] Submitted process > calling_pipeline:amrCheckpoint (7)
[1f/e05817] Submitted process > calling_pipeline:ingressCheckpoint (7)
[fc/73777c] Submitted process > fastcat (45)
[83/2733b1] Submitted process > fastcat (46)
[31/0f5026] Submitted process > calling_pipeline:perSampleReportingCheckpoint (7)
[62/856fce] Submitted process > calling_pipeline:variantCheckpoint (7)
[9c/1a9e44] Submitted process > calling_pipeline:variantCheckpoint (8)
[e7/278b56] Submitted process > calling_pipeline:amrCheckpoint (8)
[c0/3cb23f] Submitted process > calling_pipeline:perSampleReportingCheckpoint (8)
[7a/9a5994] Submitted process > fastcat (47)
[35/d96e68] Submitted process > fastcat (48)
[ab/335f73] Submitted process > calling_pipeline:ingressCheckpoint (8)
[eb/d9bed6] Submitted process > fastcat (49)
[8d/2fe611] Submitted process > calling_pipeline:variantCheckpoint (9)
[ac/2ea39a] Submitted process > calling_pipeline:ingressCheckpoint (9)
[f9/329882] Submitted process > calling_pipeline:amrCheckpoint (9)
[07/e4fda7] Submitted process > calling_pipeline:perSampleReportingCheckpoint (9)
[1d/ef1b47] Submitted process > fastcat (50)
[5e/337b7e] Submitted process > calling_pipeline:ingressCheckpoint (10)
[55/c381e6] Submitted process > fastcat (51)
[9e/2803c2] Submitted process > calling_pipeline:amrCheckpoint (10)
[41/a4b2d8] Submitted process > calling_pipeline:variantCheckpoint (10)
[26/1ab26c] Submitted process > calling_pipeline:perSampleReportingCheckpoint (10)
[89/cfdfd3] Submitted process > calling_pipeline:ingressCheckpoint (11)
[d7/19ce8a] Submitted process > calling_pipeline:variantCheckpoint (11)
[a7/91bb8d] Submitted process > calling_pipeline:amrCheckpoint (11)
[b3/d5b059] Submitted process > fastcat (52)
[46/c8ccd8] Submitted process > calling_pipeline:perSampleReportingCheckpoint (11)
[95/da2941] Submitted process > calling_pipeline:perSampleReportingCheckpoint (12)
[93/3946ad] Submitted process > fastcat (53)
[9d/f90e6b] Submitted process > calling_pipeline:variantCheckpoint (12)
[f6/623157] Submitted process > calling_pipeline:amrCheckpoint (12)
[0c/e747e4] Submitted process > calling_pipeline:ingressCheckpoint (12)
[f2/c9bf73] Submitted process > calling_pipeline:ingressCheckpoint (13)
[39/864f51] Submitted process > calling_pipeline:amrCheckpoint (13)
[e0/b1c1eb] Submitted process > fastcat (54)
[b1/1fb810] Submitted process > calling_pipeline:perSampleReportingCheckpoint (13)
[de/536bcb] Submitted process > fastcat (55)
[e1/5d2f43] Submitted process > calling_pipeline:variantCheckpoint (13)
[c3/90326a] Submitted process > fastcat (56)
[15/ada4ca] Submitted process > calling_pipeline:ingressCheckpoint (14)
[f2/fb495f] Submitted process > calling_pipeline:amrCheckpoint (14)
[98/2f8d84] Submitted process > calling_pipeline:variantCheckpoint (14)
[46/c9adc0] Submitted process > calling_pipeline:perSampleReportingCheckpoint (14)
[5e/3377be] Submitted process > calling_pipeline:ingressCheckpoint (15)
[23/b43659] Submitted process > calling_pipeline:variantCheckpoint (15)
[e4/05d3be] Submitted process > calling_pipeline:perSampleReportingCheckpoint (15)
[f2/a22fa1] Submitted process > fastcat (57)
[33/dfba67] Submitted process > calling_pipeline:amrCheckpoint (15)
[f2/0e6687] Submitted process > calling_pipeline:variantCheckpoint (16)
[b3/48c02e] Submitted process > fastcat (58)
[d2/d310a6] Submitted process > fastcat (59)
[e4/8c391e] Submitted process > calling_pipeline:ingressCheckpoint (16)
[ca/a6d3d7] Submitted process > calling_pipeline:amrCheckpoint (16)
[54/3fd85f] Submitted process > calling_pipeline:perSampleReportingCheckpoint (16)
[0d/fc3c70] Submitted process > calling_pipeline:amrCheckpoint (17)
[a1/7de0bb] Submitted process > calling_pipeline:ingressCheckpoint (17)
[da/4c73e7] Submitted process > fastcat (60)
[38/5fc209] Submitted process > calling_pipeline:variantCheckpoint (17)
[91/022ae5] Submitted process > fastcat (61)
[0d/a8104b] Submitted process > calling_pipeline:perSampleReportingCheckpoint (17)
[07/32a717] Submitted process > calling_pipeline:amrCheckpoint (18)
[8b/80df0b] Submitted process > calling_pipeline:ingressCheckpoint (18)
[76/8b4b6f] Submitted process > calling_pipeline:variantCheckpoint (18)
[cc/6e801b] Submitted process > calling_pipeline:perSampleReportingCheckpoint (18)
[15/7bbc79] Submitted process > calling_pipeline:amrCheckpoint (19)
[0c/f788e5] Submitted process > calling_pipeline:ingressCheckpoint (19)
[82/2bb48f] Submitted process > fastcat (62)
[a7/b380c2] Submitted process > calling_pipeline:variantCheckpoint (19)
[68/b27c25] Submitted process > calling_pipeline:perSampleReportingCheckpoint (19)
[31/f2f44b] Submitted process > calling_pipeline:perSampleReportingCheckpoint (20)
[05/1f8d0b] Submitted process > fastcat (63)
[b6/2ab54f] Submitted process > fastcat (64)
[88/b64547] Submitted process > calling_pipeline:variantCheckpoint (20)
[ff/9b12ed] Submitted process > calling_pipeline:ingressCheckpoint (20)
[3f/113604] Submitted process > calling_pipeline:amrCheckpoint (20)
[25/d532f3] Submitted process > calling_pipeline:perSampleReportingCheckpoint (21)
[f8/eb34a5] Submitted process > calling_pipeline:variantCheckpoint (21)
[0e/ef4490] Submitted process > fastcat (65)
[d8/a6ead8] Submitted process > calling_pipeline:ingressCheckpoint (21)
[95/03c016] Submitted process > calling_pipeline:amrCheckpoint (21)
[28/a268dd] Submitted process > fastcat (66)
[e9/1034b8] Submitted process > calling_pipeline:amrCheckpoint (22)
[55/d4a83c] Submitted process > calling_pipeline:ingressCheckpoint (22)
[1b/9a1017] Submitted process > fastcat (67)
[dd/eefc1b] Submitted process > calling_pipeline:perSampleReportingCheckpoint (22)
[5e/4a0431] Submitted process > calling_pipeline:variantCheckpoint (22)
[5f/25abec] Submitted process > calling_pipeline:amrCheckpoint (23)
[4d/c0d61f] Submitted process > calling_pipeline:variantCheckpoint (23)
[9e/782fe9] Submitted process > fastcat (68)
[cf/e9afd8] Submitted process > calling_pipeline:perSampleReportingCheckpoint (23)
[21/43c40c] Submitted process > fastcat (69)
[c3/036f0f] Submitted process > calling_pipeline:ingressCheckpoint (23)
[a7/8eea1d] Submitted process > calling_pipeline:ingressCheckpoint (24)
[52/7d48e7] Submitted process > calling_pipeline:variantCheckpoint (24)
[35/980b57] Submitted process > calling_pipeline:amrCheckpoint (24)
[ff/d8a3e8] Submitted process > fastcat (70)
[14/3dab15] Submitted process > calling_pipeline:perSampleReportingCheckpoint (24)
[01/aca2dc] Submitted process > fastcat (71)
[a2/70ff7c] Submitted process > calling_pipeline:perSampleReportingCheckpoint (25)
[0c/fefbe1] Submitted process > calling_pipeline:amrCheckpoint (25)
[80/b4b13c] Submitted process > calling_pipeline:ingressCheckpoint (25)
[75/f31eae] Submitted process > calling_pipeline:variantCheckpoint (25)
[8a/c21f57] Submitted process > fastcat (72)
[f5/6328a8] Submitted process > calling_pipeline:ingressCheckpoint (26)
[ed/5d7c22] Submitted process > calling_pipeline:amrCheckpoint (26)
[55/0170ee] Submitted process > calling_pipeline:variantCheckpoint (26)
[aa/abe157] Submitted process > calling_pipeline:perSampleReportingCheckpoint (26)
[92/4af525] Submitted process > fastcat (73)
[f2/e0409b] Submitted process > calling_pipeline:variantCheckpoint (27)
[4f/b05a77] Submitted process > fastcat (74)
[26/6a0b80] Submitted process > calling_pipeline:ingressCheckpoint (27)
[ce/eecd21] Submitted process > calling_pipeline:amrCheckpoint (27)
[8f/acacce] Submitted process > calling_pipeline:perSampleReportingCheckpoint (27)
[d4/0e9115] Submitted process > fastcat (75)
[d2/c973a9] Submitted process > calling_pipeline:ingressCheckpoint (28)
[52/fb164f] Submitted process > calling_pipeline:amrCheckpoint (28)
[bf/525d20] Submitted process > calling_pipeline:perSampleReportingCheckpoint (28)
[66/221f6e] Submitted process > calling_pipeline:variantCheckpoint (28)
[12/91abbb] Submitted process > calling_pipeline:variantCheckpoint (29)
[4c/13acb1] Submitted process > calling_pipeline:perSampleReportingCheckpoint (29)
[7e/398520] Submitted process > fastcat (76)
[fa/77144e] Submitted process > fastcat (77)
[37/8484c7] Submitted process > calling_pipeline:amrCheckpoint (29)
[5b/02ff2f] Submitted process > calling_pipeline:ingressCheckpoint (29)
[02/378976] Submitted process > calling_pipeline:amrCheckpoint (30)
[18/8b77be] Submitted process > fastcat (78)
[a2/cfabb0] Submitted process > calling_pipeline:ingressCheckpoint (30)
[59/c9c2b2] Submitted process > calling_pipeline:perSampleReportingCheckpoint (30)
[60/14ee7e] Submitted process > calling_pipeline:variantCheckpoint (30)
[93/474aa4] Submitted process > calling_pipeline:variantCheckpoint (31)
[7a/5ec7ce] Submitted process > fastcat (79)
[72/a68d93] Submitted process > calling_pipeline:perSampleReportingCheckpoint (31)
[40/54d442] Submitted process > fastcat (80)
[2b/f3ffa1] Submitted process > calling_pipeline:amrCheckpoint (31)
[6f/df16dd] Submitted process > calling_pipeline:ingressCheckpoint (31)
[4b/9afafb] Submitted process > calling_pipeline:perSampleReportingCheckpoint (32)
[45/1f49c1] Submitted process > calling_pipeline:amrCheckpoint (32)
[da/69242e] Submitted process > calling_pipeline:variantCheckpoint (32)
[83/e4cac3] Submitted process > fastcat (81)
[77/e666c1] Submitted process > calling_pipeline:ingressCheckpoint (32)
[f6/1624c1] Submitted process > calling_pipeline:variantCheckpoint (33)
[f4/bc9beb] Submitted process > calling_pipeline:ingressCheckpoint (33)
[65/c82756] Submitted process > calling_pipeline:perSampleReportingCheckpoint (33)
[f4/436873] Submitted process > fastcat (82)
[a4/474403] Submitted process > calling_pipeline:amrCheckpoint (33)
[1e/4d9664] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (4)
[b1/5a4bfc] Submitted process > calling_pipeline:ingressCheckpoint (34)
[05/022b22] Submitted process > calling_pipeline:perSampleReportingCheckpoint (34)
[af/bc2316] Submitted process > calling_pipeline:variantCheckpoint (34)
[a5/35c283] Submitted process > calling_pipeline:amrCheckpoint (34)
[68/fcda2a] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (5)
[93/b4756a] Submitted process > calling_pipeline:variantCheckpoint (35)
[8c/ad912e] Submitted process > calling_pipeline:perSampleReportingCheckpoint (35)
[7d/06df11] Submitted process > calling_pipeline:amrCheckpoint (35)
[57/181d26] Submitted process > calling_pipeline:ingressCheckpoint (35)
[e6/9768d5] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (6)
[66/3d6fe1] Submitted process > calling_pipeline:perSampleReportingCheckpoint (36)
[3b/e4f871] Submitted process > calling_pipeline:ingressCheckpoint (36)
[55/742e88] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (7)
[3f/5d3d53] Submitted process > calling_pipeline:amrCheckpoint (36)
[66/449cba] Submitted process > calling_pipeline:variantCheckpoint (36)
[c9/b9a6b8] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (8)
[2d/5cd4ff] Submitted process > calling_pipeline:ingressCheckpoint (37)
[54/4c2d31] Submitted process > calling_pipeline:perSampleReportingCheckpoint (37)
[16/0b4fd3] Submitted process > calling_pipeline:amrCheckpoint (37)
[a9/707ea1] Submitted process > calling_pipeline:variantCheckpoint (37)
[f9/f77fe8] Submitted process > calling_pipeline:variantCheckpoint (38)
[00/26aeb9] Submitted process > calling_pipeline:amrCheckpoint (38)
[c6/70345e] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (9)
[56/f13f7a] Submitted process > calling_pipeline:ingressCheckpoint (38)
[31/6228b4] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (10)
[28/0247b9] Submitted process > calling_pipeline:perSampleReportingCheckpoint (38)
[ef/15863b] Submitted process > calling_pipeline:ingressCheckpoint (39)
[b8/85b6be] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (11)
[c5/7ad1ac] Submitted process > calling_pipeline:perSampleReportingCheckpoint (39)
[08/8d4a54] Submitted process > calling_pipeline:amrCheckpoint (39)
[eb/ecfec7] Submitted process > calling_pipeline:variantCheckpoint (39)
[f4/5ec54a] Submitted process > calling_pipeline:amrCheckpoint (40)
[d3/647e50] Submitted process > calling_pipeline:ingressCheckpoint (40)
[bd/a927df] Submitted process > calling_pipeline:variantCheckpoint (40)
[a1/6d32fe] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (12)
[30/9b7aca] Submitted process > calling_pipeline:perSampleReportingCheckpoint (40)
[93/dbc782] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (13)
[59/6c39c9] Submitted process > calling_pipeline:ingressCheckpoint (41)
[46/f98466] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (14)
[20/290f85] Submitted process > calling_pipeline:variantCheckpoint (41)
[71/b63c6c] Submitted process > calling_pipeline:perSampleReportingCheckpoint (41)
[db/94345e] Submitted process > calling_pipeline:amrCheckpoint (41)
[a1/830042] Submitted process > calling_pipeline:perSampleReportingCheckpoint (42)
[60/4c923a] Submitted process > calling_pipeline:variantCheckpoint (42)
[6d/21b747] Submitted process > calling_pipeline:amrCheckpoint (42)
[61/34796c] Submitted process > calling_pipeline:ingressCheckpoint (42)
[fc/00c2af] Submitted process > calling_pipeline:variantCheckpoint (43)
[8c/866e7a] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (15)
[53/bb9831] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (16)
[f4/589629] Submitted process > calling_pipeline:amrCheckpoint (43)
[e2/970526] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (17)
[51/1cdd62] Submitted process > calling_pipeline:perSampleReportingCheckpoint (43)
[b0/76ca46] Submitted process > calling_pipeline:ingressCheckpoint (43)
[cb/d9f077] Submitted process > calling_pipeline:ingressCheckpoint (44)
[a1/82d663] Submitted process > calling_pipeline:variantCheckpoint (44)
[25/49529d] Submitted process > calling_pipeline:amrCheckpoint (44)
[9f/a759f9] Submitted process > calling_pipeline:perSampleReportingCheckpoint (44)
[79/2042e2] Submitted process > calling_pipeline:ingressCheckpoint (45)
[69/61a38d] Submitted process > calling_pipeline:perSampleReportingCheckpoint (45)
[7c/9022cf] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (18)
[d2/06aff6] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (19)
[41/e5420a] Submitted process > calling_pipeline:variantCheckpoint (45)
[aa/d73877] Submitted process > calling_pipeline:amrCheckpoint (45)
[33/963310] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (20)
[e6/ba5590] Submitted process > calling_pipeline:variantCheckpoint (46)
[b6/b82bf8] Submitted process > calling_pipeline:ingressCheckpoint (46)
[73/13bf71] Submitted process > calling_pipeline:amrCheckpoint (46)
[47/8bb017] Submitted process > calling_pipeline:perSampleReportingCheckpoint (46)
[2e/8c13e1] Submitted process > calling_pipeline:amrCheckpoint (47)
[5a/e3cb41] Submitted process > calling_pipeline:ingressCheckpoint (47)
[66/8f3cf6] Submitted process > calling_pipeline:perSampleReportingCheckpoint (47)
[c6/bf3dfc] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (21)
[78/f3e656] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (22)
[47/75e1c1] Submitted process > calling_pipeline:variantCheckpoint (47)
[7e/144018] Submitted process > calling_pipeline:ingressCheckpoint (48)
[bc/f27ab7] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (23)
[ae/4c148b] Submitted process > calling_pipeline:perSampleReportingCheckpoint (48)
[e8/2c0c6d] Submitted process > calling_pipeline:variantCheckpoint (48)
[e6/c4344e] Submitted process > calling_pipeline:amrCheckpoint (48)
[15/662688] Submitted process > calling_pipeline:ingressCheckpoint (49)
[80/ca5738] Submitted process > calling_pipeline:amrCheckpoint (49)
[11/98a765] Submitted process > calling_pipeline:variantCheckpoint (49)
[a5/315f81] Submitted process > calling_pipeline:perSampleReportingCheckpoint (49)
[b0/fc2d7a] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (24)
[48/9db93b] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (25)
[59/802c83] Submitted process > calling_pipeline:amrCheckpoint (50)
[25/7cfcc1] Submitted process > calling_pipeline:variantCheckpoint (50)
[b4/89361d] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (26)
[69/a3930f] Submitted process > calling_pipeline:perSampleReportingCheckpoint (50)
[f1/db5a53] Submitted process > calling_pipeline:ingressCheckpoint (50)
[28/01dc07] Submitted process > calling_pipeline:variantCheckpoint (51)
[9a/81ec12] Submitted process > calling_pipeline:perSampleReportingCheckpoint (51)
[61/0a1a79] Submitted process > calling_pipeline:ingressCheckpoint (51)
[c6/db001f] Submitted process > calling_pipeline:amrCheckpoint (51)
[22/2d59da] Submitted process > calling_pipeline:perSampleReportingCheckpoint (52)
[6f/369cfc] Submitted process > calling_pipeline:amrCheckpoint (52)
[7a/b79c83] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (27)
[55/1135ba] Submitted process > calling_pipeline:variantCheckpoint (52)
[2c/e207eb] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (28)
[fd/7c2e29] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (29)
[90/21998a] Submitted process > calling_pipeline:ingressCheckpoint (52)
[bc/364514] Submitted process > calling_pipeline:perSampleReportingCheckpoint (53)
[62/29e6d4] Submitted process > calling_pipeline:amrCheckpoint (53)
[5c/07aae6] Submitted process > calling_pipeline:variantCheckpoint (53)
[a0/ffe64c] Submitted process > calling_pipeline:ingressCheckpoint (53)
[b3/fca753] Submitted process > calling_pipeline:perSampleReportingCheckpoint (54)
[c8/2d357b] Submitted process > calling_pipeline:amrCheckpoint (54)
[1f/516b3f] Submitted process > calling_pipeline:variantCheckpoint (54)
[2c/d8f217] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (30)
[98/eca653] Submitted process > calling_pipeline:mlstVersion
[2e/23e6ea] Submitted process > calling_pipeline:ingressCheckpoint (54)
[d1/9fd02b] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (31)
[65/952be1] Submitted process > calling_pipeline:ingressCheckpoint (55)
[bd/9c5c61] Submitted process > calling_pipeline:perSampleReportingCheckpoint (55)
[c0/e36ea7] Submitted process > calling_pipeline:amrCheckpoint (55)
[b7/6282db] Submitted process > calling_pipeline:variantCheckpoint (55)
[9a/5ed84c] Submitted process > calling_pipeline:perSampleReportingCheckpoint (56)
[c4/085412] Submitted process > calling_pipeline:amrCheckpoint (56)
[51/1dbb88] Submitted process > calling_pipeline:ingressCheckpoint (56)
[f4/999959] Submitted process > calling_pipeline:variantCheckpoint (56)
[4f/f37da5] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (32)
[ff/dfcfd6] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (33)
[42/4198b3] Submitted process > calling_pipeline:ingressCheckpoint (57)
[6c/8893da] Submitted process > calling_pipeline:perSampleReportingCheckpoint (57)
[f0/078100] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (34)
[41/8e793e] Submitted process > calling_pipeline:variantCheckpoint (57)
[a5/610ef0] Submitted process > calling_pipeline:amrCheckpoint (57)
[c1/c0bdda] Submitted process > calling_pipeline:amrCheckpoint (58)
[47/a5639e] Submitted process > calling_pipeline:ingressCheckpoint (58)
[35/051467] Submitted process > calling_pipeline:perSampleReportingCheckpoint (58)
[1a/3449b9] Submitted process > calling_pipeline:variantCheckpoint (58)
[7d/1c0c4a] Submitted process > calling_pipeline:perSampleReportingCheckpoint (59)
[72/f98a08] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (35)
[76/334d22] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (36)
[5f/f35d15] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (37)
[f7/3a0b5d] Submitted process > calling_pipeline:variantCheckpoint (59)
[18/2b7a60] Submitted process > calling_pipeline:amrCheckpoint (59)
[17/572c0b] Submitted process > calling_pipeline:ingressCheckpoint (59)
[9b/660124] Submitted process > calling_pipeline:perSampleReportingCheckpoint (60)
[75/56dbb4] Submitted process > calling_pipeline:amrCheckpoint (60)
[e0/6df6db] Submitted process > calling_pipeline:variantCheckpoint (60)
[6a/e9bd7d] Submitted process > calling_pipeline:ingressCheckpoint (60)
[77/6ee76f] Submitted process > calling_pipeline:perSampleReportingCheckpoint (61)
[0a/57cfd3] Submitted process > calling_pipeline:ingressCheckpoint (61)
[9b/472a14] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (38)
[fa/2a919d] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (39)
[c0/1063ec] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (40)
[e7/084a04] Submitted process > calling_pipeline:variantCheckpoint (61)
[87/f1eee6] Submitted process > calling_pipeline:amrCheckpoint (61)
[91/40d200] Submitted process > calling_pipeline:perSampleReportingCheckpoint (62)
[8a/75e328] Submitted process > calling_pipeline:variantCheckpoint (62)
[50/d9b5ef] Submitted process > calling_pipeline:amrCheckpoint (62)
[43/7e0887] Submitted process > calling_pipeline:ingressCheckpoint (62)
[3e/d1ecc5] Submitted process > calling_pipeline:ingressCheckpoint (63)
[64/5b37fb] Submitted process > calling_pipeline:amrCheckpoint (63)
[fc/7d6523] Submitted process > calling_pipeline:perSampleReportingCheckpoint (63)
[cc/5a88ca] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (41)
[e1/5bad1d] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (42)
[c6/fb58a0] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (43)
[0f/d0ae14] Submitted process > calling_pipeline:variantCheckpoint (63)
[1b/1cae16] Submitted process > calling_pipeline:amrCheckpoint (64)
[53/c8aec8] Submitted process > calling_pipeline:perSampleReportingCheckpoint (64)
[aa/015196] Submitted process > calling_pipeline:variantCheckpoint (64)
[5c/94e258] Submitted process > calling_pipeline:ingressCheckpoint (64)
[e9/6eed42] Submitted process > calling_pipeline:amrCheckpoint (65)
[82/97d55e] Submitted process > calling_pipeline:perSampleReportingCheckpoint (65)
[23/80b0bc] Submitted process > calling_pipeline:ingressCheckpoint (65)
[c4/d436da] Submitted process > calling_pipeline:variantCheckpoint (65)
[f8/4b86f8] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (44)
[eb/982810] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (45)
[ab/31bba7] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (46)
[8b/105f7b] Submitted process > calling_pipeline:variantCheckpoint (66)
[eb/2c744d] Submitted process > calling_pipeline:amrCheckpoint (66)
[d4/876f76] Submitted process > calling_pipeline:perSampleReportingCheckpoint (66)
[44/0c789b] Submitted process > calling_pipeline:ingressCheckpoint (66)
[5e/aea7f2] Submitted process > calling_pipeline:variantCheckpoint (67)
[d3/4b2592] Submitted process > calling_pipeline:amrCheckpoint (67)
[30/647991] Submitted process > calling_pipeline:ingressCheckpoint (67)
[93/0401f0] Submitted process > calling_pipeline:perSampleReportingCheckpoint (67)
[f4/2280c2] Submitted process > calling_pipeline:amrCheckpoint (68)
[d4/4a462b] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (47)
[96/ff2fff] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (48)
[05/56f3a2] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (49)
[fd/aa0c72] Submitted process > calling_pipeline:perSampleReportingCheckpoint (68)
[70/3a3d1b] Submitted process > calling_pipeline:ingressCheckpoint (68)
[4e/623b87] Submitted process > calling_pipeline:variantCheckpoint (68)
[20/9541d1] Submitted process > calling_pipeline:variantCheckpoint (69)
[a8/93bcf1] Submitted process > calling_pipeline:perSampleReportingCheckpoint (69)
[e7/33f503] Submitted process > calling_pipeline:ingressCheckpoint (69)
[f0/4a4b79] Submitted process > calling_pipeline:amrCheckpoint (69)
[f0/1794a7] Submitted process > calling_pipeline:ingressCheckpoint (70)
[81/f597b3] Submitted process > calling_pipeline:perSampleReportingCheckpoint (70)
[a9/84d03c] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (50)
[2b/78ad28] Submitted process > calling_pipeline:variantCheckpoint (70)
[2d/c5a8de] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (51)
[71/75de78] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (52)
[f9/210957] Submitted process > calling_pipeline:amrCheckpoint (70)
[5c/f83909] Submitted process > calling_pipeline:variantCheckpoint (71)
[fc/1bb51b] Submitted process > calling_pipeline:ingressCheckpoint (71)
[97/b4024b] Submitted process > calling_pipeline:perSampleReportingCheckpoint (71)
[36/9c3253] Submitted process > calling_pipeline:amrCheckpoint (71)
[b7/ebc23a] Submitted process > calling_pipeline:ingressCheckpoint (72)
[2e/eecf78] Submitted process > calling_pipeline:amrCheckpoint (72)
[ac/694ceb] Submitted process > calling_pipeline:variantCheckpoint (72)
[20/260c45] Submitted process > calling_pipeline:perSampleReportingCheckpoint (72)
[02/9cfffb] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (53)
[d9/657890] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (54)
[05/639ee8] Submitted process > calling_pipeline:variantCheckpoint (73)
[db/33efdd] Submitted process > calling_pipeline:perSampleReportingCheckpoint (73)
[b2/18c237] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (55)
[e5/b043f2] Submitted process > calling_pipeline:amrCheckpoint (73)
[49/feebe0] Submitted process > calling_pipeline:ingressCheckpoint (73)
[52/3df4f3] Submitted process > calling_pipeline:variantCheckpoint (74)
[3c/067b85] Submitted process > calling_pipeline:perSampleReportingCheckpoint (74)
[10/b09bd0] Submitted process > calling_pipeline:amrCheckpoint (74)
[41/6f32de] Submitted process > calling_pipeline:ingressCheckpoint (74)
[b0/431dcb] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (56)
[d7/f09032] Submitted process > calling_pipeline:variantCheckpoint (75)
[3d/74ef72] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (57)
[aa/945e2a] Submitted process > calling_pipeline:perSampleReportingCheckpoint (75)
[a0/a72c86] Submitted process > calling_pipeline:ingressCheckpoint (75)
[5c/54cdae] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (58)
[08/06ef49] Submitted process > calling_pipeline:amrCheckpoint (75)
[c0/f88fae] Submitted process > calling_pipeline:perSampleReportingCheckpoint (76)
[a1/943bcb] Submitted process > calling_pipeline:ingressCheckpoint (76)
[4e/85db53] Submitted process > calling_pipeline:amrCheckpoint (76)
[8e/b9fb81] Submitted process > calling_pipeline:variantCheckpoint (76)
[4a/c17f9a] Submitted process > calling_pipeline:variantCheckpoint (77)
[42/f6248e] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (59)
[19/c9965d] Submitted process > calling_pipeline:ingressCheckpoint (77)
[6d/e207a0] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (60)
[6b/d90801] Submitted process > calling_pipeline:amrCheckpoint (77)
[58/85c352] Submitted process > calling_pipeline:perSampleReportingCheckpoint (77)
[4d/badf7c] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (61)
[4c/b19571] Submitted process > calling_pipeline:variantCheckpoint (78)
[0e/76eed6] Submitted process > calling_pipeline:perSampleReportingCheckpoint (78)
[79/23f245] Submitted process > calling_pipeline:ingressCheckpoint (78)
[13/61982e] Submitted process > calling_pipeline:amrCheckpoint (78)
[cb/c51fa3] Submitted process > calling_pipeline:variantCheckpoint (79)
[cb/1cc1b1] Submitted process > calling_pipeline:ingressCheckpoint (79)
[ca/7325c4] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (62)
[de/714648] Submitted process > calling_pipeline:perSampleReportingCheckpoint (79)
[5b/b5cba9] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (63)
[e2/0f9f27] Submitted process > calling_pipeline:amrCheckpoint (79)
[b4/6f9e6d] Submitted process > calling_pipeline:ingressCheckpoint (80)
[44/f84289] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (64)
[c6/17c74a] Submitted process > calling_pipeline:variantCheckpoint (80)
[64/ec40ad] Submitted process > calling_pipeline:perSampleReportingCheckpoint (80)
[39/1f1656] Submitted process > calling_pipeline:amrCheckpoint (80)
[75/69ef0f] Submitted process > calling_pipeline:amrCheckpoint (81)
[7b/540b76] Submitted process > calling_pipeline:perSampleReportingCheckpoint (81)
[f3/9a2d1a] Submitted process > calling_pipeline:ingressCheckpoint (81)
[62/34db15] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (65)
[2f/f27e19] Submitted process > calling_pipeline:variantCheckpoint (81)
[e3/1b15b2] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (66)
[4a/282604] Submitted process > calling_pipeline:ingressCheckpoint (82)
[56/fd1481] Submitted process > calling_pipeline:perSampleReportingCheckpoint (82)
[14/85e589] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (67)
[6c/5e5c76] Submitted process > calling_pipeline:variantCheckpoint (82)
[bc/65646a] Submitted process > calling_pipeline:amrCheckpoint (82)
[85/e0afb6] Submitted process > calling_pipeline:accumulateCheckpoints (1)
[d5/5a8f30] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (68)
[3f/c94a5b] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (69)
[43/b1c3f4] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (70)
[88/de30a9] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (71)
[7e/ce0f1d] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (72)
[d3/791a54] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (73)
[0f/6e1f93] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (74)
[7b/4d1632] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (75)
[04/f0489a] Submitted process > calling_pipeline:accumulateCheckpoints (2)
[35/5ba557] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (76)
[32/3d4225] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (77)
[00/8502b0] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (78)
[37/1ffe2a] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (79)
[bb/4b1010] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (80)
[5b/010ee7] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (81)
[a7/8a79e6] Submitted process > calling_pipeline:collectFastqIngressResultsInDir (82)
[fe/e0173b] Submitted process > calling_pipeline:getVersions
[fd/680d59] Submitted process > calling_pipeline:accumulateCheckpoints (3)
[6d/5dc36f] Submitted process > calling_pipeline:deNovo (1)
[7f/d10bac] Submitted process > calling_pipeline:deNovo (2)
[78/458f0e] Submitted process > calling_pipeline:deNovo (3)
[5a/c575f3] Submitted process > calling_pipeline:deNovo (4)
WARN: Flye failed for sample 'barcode04' due to low coverage.
[29/4fe017] Submitted process > calling_pipeline:deNovo (5)
WARN: Flye failed for sample 'barcode05' due to low coverage.
[98/daad81] Submitted process > calling_pipeline:deNovo (6)
WARN: Flye failed for sample 'barcode03' due to low coverage.
WARN: Flye failed for sample 'barcode06' due to low coverage.
[d6/348376] Submitted process > calling_pipeline:deNovo (7)
WARN: Flye failed for sample 'barcode07' due to low coverage.
[fe/f81427] Submitted process > calling_pipeline:deNovo (8)
[6d/291aa4] Submitted process > calling_pipeline:deNovo (9)
WARN: Flye failed for sample 'barcode09' due to low coverage.
[4a/d12e6c] Submitted process > calling_pipeline:deNovo (10)
WARN: Flye failed for sample 'barcode10' due to low coverage.
[85/1a5916] Submitted process > calling_pipeline:deNovo (11)
[02/3add1d] Submitted process > calling_pipeline:deNovo (12)
WARN: Flye failed for sample 'barcode12' due to low coverage.
[f4/ad798a] Submitted process > calling_pipeline:deNovo (13)
WARN: Flye failed for sample 'barcode13' due to low coverage.
[dd/cb02be] Submitted process > calling_pipeline:deNovo (14)
WARN: Flye failed for sample 'barcode15' due to low coverage.
[59/069145] Submitted process > calling_pipeline:deNovo (15)
[04/64164c] Submitted process > calling_pipeline:deNovo (16)
WARN: Flye failed for sample 'barcode17' due to low coverage.
[b7/394803] Submitted process > calling_pipeline:deNovo (17)
[5f/eb2860] Submitted process > calling_pipeline:deNovo (18)
[c9/8cf992] Submitted process > calling_pipeline:deNovo (19)
WARN: Flye failed for sample 'barcode20' due to low coverage.
[27/f8845b] Submitted process > calling_pipeline:deNovo (20)
WARN: Flye failed for sample 'barcode21' due to low coverage.
[6d/0d9e9b] Submitted process > calling_pipeline:deNovo (21)
WARN: Flye failed for sample 'barcode22' due to low coverage.
[c8/372afa] Submitted process > calling_pipeline:deNovo (22)
WARN: Flye failed for sample 'barcode24' due to low coverage.
[81/e3f3bb] Submitted process > calling_pipeline:deNovo (23)
[23/675ff9] Submitted process > calling_pipeline:deNovo (24)
WARN: Flye failed for sample 'barcode26' due to low coverage.
[3c/5a2ab2] Submitted process > calling_pipeline:deNovo (25)
[c1/91d46a] Submitted process > calling_pipeline:deNovo (26)
WARN: Flye failed for sample 'barcode25' due to low coverage.
[b5/a73599] Submitted process > calling_pipeline:deNovo (27)
WARN: Flye failed for sample 'barcode27' due to low coverage.
WARN: Flye failed for sample 'barcode28' due to low coverage.
[40/beebff] Submitted process > calling_pipeline:deNovo (28)
WARN: Flye failed for sample 'barcode29' due to low coverage.
[2e/916d5e] Submitted process > calling_pipeline:deNovo (29)
WARN: Flye failed for sample 'barcode31' due to low coverage.
[ae/01e1fb] Submitted process > calling_pipeline:deNovo (30)
WARN: Flye failed for sample 'barcode32' due to low coverage.
[3d/2cebeb] Submitted process > calling_pipeline:deNovo (31)
WARN: Flye failed for sample 'barcode33' due to low coverage.
[65/fe94d0] Submitted process > calling_pipeline:deNovo (32)
WARN: Flye failed for sample 'barcode35' due to low coverage.
[fb/5d13ce] Submitted process > calling_pipeline:deNovo (33)
[5a/f8b9ed] Submitted process > calling_pipeline:deNovo (34)
WARN: Flye failed for sample 'barcode37' due to low coverage.
WARN: Flye failed for sample 'barcode36' due to low coverage.
[ec/53fee7] Submitted process > calling_pipeline:deNovo (35)
[4a/18e414] Submitted process > calling_pipeline:deNovo (36)
WARN: Flye failed for sample 'barcode41' due to low coverage.
[b9/8507aa] Submitted process > calling_pipeline:deNovo (37)
[78/8b052a] Submitted process > calling_pipeline:deNovo (38)
[c2/afcba5] Submitted process > calling_pipeline:deNovo (39)
[22/0bc659] Submitted process > calling_pipeline:deNovo (40)
[94/944957] Submitted process > calling_pipeline:deNovo (41)
WARN: Flye failed for sample 'barcode44' due to low coverage.
[50/391f19] Submitted process > calling_pipeline:deNovo (42)
WARN: Flye failed for sample 'barcode45' due to low coverage.
[16/cba003] Submitted process > calling_pipeline:deNovo (43)
[7a/3022dc] Submitted process > calling_pipeline:deNovo (44)
[f6/2e420c] Submitted process > calling_pipeline:deNovo (45)
WARN: Flye failed for sample 'barcode46' due to low coverage.
[35/7509f1] Submitted process > calling_pipeline:deNovo (46)
ERROR ~ Error executing process > 'calling_pipeline:deNovo (45)'
Caused by:
Process `calling_pipeline:deNovo (45)` terminated with an error exit status (1)
Command executed:
COV_FAIL=0
FLYE_EXIT_CODE=0
flye --nano-hq reads.fastq.gz --out-dir output --threads "3" || FLYE_EXIT_CODE=$?
if [[ $FLYE_EXIT_CODE -eq 0 ]]; then
mv output/assembly.fasta "./barcode47.draft_assembly.fasta"
mv output/assembly_info.txt "./barcode47_flye_stats.tsv"
bgzip "barcode47.draft_assembly.fasta"
else
# flye failed --> check the log to check why
edge_cov=$(
grep -oP 'Mean edge coverage: \K\d+' output/flye.log || echo 5
)
ovlp_cov=$(
grep -oP 'Overlap-based coverage: \K\d+' output/flye.log || echo 5
)
if [[
$edge_cov -lt 5 ||
$ovlp_cov -lt 5
]]; then
echo -n "Caught Flye failure due to low coverage (either mean edge cov. or "
echo "overlap-based cov. were below 5)".
COV_FAIL=1
elif grep -q "No disjointigs were assembled" output/flye.log; then
echo -n "Caught Flye failure due to disjointig assembly."
COV_FAIL=2
else
# exit a subshell with error so that the process fails
( exit $FLYE_EXIT_CODE )
fi
fi
Command exit status:
1
Command output:
(empty)
Command error:
[2024-10-17 10:24:24] INFO: Starting Flye 2.9.3-b1797
[2024-10-17 10:24:24] INFO: >>>STAGE: configure
[2024-10-17 10:24:24] INFO: Configuring run
[2024-10-17 10:24:24] INFO: Total read length: 9712
[2024-10-17 10:24:24] INFO: Reads N50/N90: 9712 / 9712
[2024-10-17 10:24:24] INFO: Minimum overlap set to 10000
[2024-10-17 10:24:24] INFO: >>>STAGE: assembly
[2024-10-17 10:24:24] INFO: Assembling disjointigs
[2024-10-17 10:24:24] INFO: Reading sequences
[2024-10-17 10:24:24] INFO: Building minimizer index
[2024-10-17 10:24:24] INFO: Pre-calculating index storage
[2024-10-17 10:24:24] INFO: Filling index
[2024-10-17 10:24:24] ERROR: Command '['flye-modules', 'assemble', '--reads', 'reads.fastq.gz', '--out-asm', 'output/00-assembly/draft_assembly.fasta', '--config', '/home/epi2melabs/conda/lib/python3.8/site-packages/flye/config/bin_cfg/asm_nano_hq.cfg', '--log', 'output/flye.log', '--threads', '3', '--min-ovlp', '10000']' died with <Signals.SIGFPE: 8>.
[2024-10-17 10:24:24] ERROR: Pipeline aborted
Work dir:
/mnt/c/Users/Sequencing/epi2melabs/instances/wf-bacterial-genomes_01JACZ50KNN6EF71EKC6551GPZ/work/f6/2e420c9a30e20df715e5fddae210f8
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '/mnt/c/Users/Sequencing/epi2melabs/instances/wf-bacterial-genomes_01JACZ50KNN6EF71EKC6551GPZ/nextflow.log' file for details
WARN: Killing running tasks (1)

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 @AnjaliSM22 - it looks like its erroring on a particular sample that only has 1 read in it (after filtering for reads <1kb), does this sound right?