ERROR ~ Error executing process > 'cnv_spectre:callCNV (1)'

[nikelau]

Operating System

Windows 11

Other Linux

No response

Workflow Version

v2.2.6

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

V5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

ERROR ~ Error executing process > 'cnv_spectre:callCNV (1)'

I am running this workflow on another computer using the same configurations and input files as the other error request with sniffles.

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/d/epi2melabs/workflows/epi2me-labs/wf-human-variation/main.nf` [keen_franklin] DSL2 - revision: ce2f386d8a
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-human-variation v2.2.6
--------------------------------------------------------------------------------
Core Nextflow options
  runName         : keen_franklin
  containerEngine : docker
  container       : ontresearch/wf-human-variation:sha2b856c1f358ddf1576217a336bc0e9864b6dc0ed
  launchDir       : /mnt/d/epi2melabs/instances/wf-human-variation_01J2JDMS09VVSZDYG8QTMXKH51
  workDir         : /mnt/d/epi2melabs/instances/wf-human-variation_01J2JDMS09VVSZDYG8QTMXKH51/work
  projectDir      : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-human-variation
  userName        : epi2mewsl
  profile         : standard
  configFiles     : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-human-variation/nextflow.config, /mnt/d/epi2melabs/instances/wf-human-variation_01J2JDMS09VVSZDYG8QTMXKH51/local.config
Workflow Options
  sv              : true
  snp             : true
  cnv             : true
  mod             : true
Main options
  sample_name     : 23C8111791_DMPK
  bam             : /mnt/c/NanoporeRun/20240708_MIN_AdpSam_STR/23C8111791_DMPK/bam_files
  ref             : /mnt/c/EPI2ME_input/reference_genomes/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
  basecaller_cfg  : dna_r9.4.1_e8_hac@v3.3
  bam_min_coverage: 0
  bed             : /mnt/c/EPI2ME_input/_bedFiles_hg38/combined_STR_Dark_PGx_MT_modified.bed
  phased          : true
  out_dir         : /mnt/d/epi2melabs/instances/wf-human-variation_01J2JDMS09VVSZDYG8QTMXKH51/output
Structural variant calling options
  tr_bed          : /mnt/c/EPI2ME_input/_TrBed_for_SV/GRCh38/original/human_GRCh38_no_alt_analysis_set.trf.bed
Multiprocessing Options
  threads         : 18
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-human-variation for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-human-variation v2.2.6.
--------------------------------------------------------------------------------
Searching input for [.bam, .ubam] files.
WARN: Inferring genetic sex of sample as params.sex was not provided.
[ff/739b98] Submitted process > ingress:checkBamHeaders (1)
[3b/a06788] Submitted process > report_snp:getParams
[3a/ccf7f4] Submitted process > getVersions
[a2/45a382] Submitted process > getParams
[56/f31ec7] Submitted process > sv:runReport:getParams
[aa/b7b9f0] Submitted process > report_snp:getVersions
[04/9a64a2] Submitted process > cnv_spectre:getVersions
[a3/6590dc] Submitted process > cnv_spectre:getParams
[68/186f20] Submitted process > sv:runReport:getVersions
[f4/c90f36] Submitted process > cram_cache (1)
[33/a9fd74] Submitted process > ingress:validateIndex (1)
[ad/4cd701] Submitted process > cnv_spectre:add_snp_tools_to_versions
[4e/ea69f9] Submitted process > ingress:check_for_alignment (1)
[4f/044112] Submitted process > getGenome (1)
[40/67e9c7] Submitted process > sanitise_bed (1)
[6e/22b744] Submitted process > readStats (1)
[1c/17310e] Submitted process > mosdepth_input (1)
[cb/bd2c7a] Submitted process > infer_sex (1)
[88/80fdfb] Submitted process > publish_artifact (3)
[da/b7daeb] Submitted process > publish_artifact (1)
[93/3eebb9] Submitted process > publish_artifact (2)
[b4/8fc724] Submitted process > publish_artifact (4)
[0a/1f9ceb] Submitted process > publish_artifact (5)
[10/0b8f67] Submitted process > publish_artifact (6)
[cc/402b95] Submitted process > lookup_clair3_model (1)
[dd/f31622] Submitted process > validate_modbam (1)
[48/92624c] Submitted process > cnv_spectre:mosdepth (1)
[a3/0d9db0] Submitted process > makeAlignmentReport
[bf/2de3de] Submitted process > sample_probs (1)
Autoselected Clair3 model: r941_prom_sup_g5014
[1e/966506] Submitted process > snp:make_chunks (1)
[cb/27d857] Submitted process > publish_artifact (7)
[0a/51a953] Submitted process > snp:pileup_variants (9)
[aa/c985ca] Submitted process > snp:pileup_variants (6)
[70/578329] Submitted process > snp:pileup_variants (3)
[b2/7a93a1] Submitted process > snp:pileup_variants (7)
[18/daa380] Submitted process > snp:pileup_variants (13)
[f7/b0cf6f] Submitted process > snp:pileup_variants (18)
[26/8fc2f4] Submitted process > snp:pileup_variants (11)
[e3/e128a4] Submitted process > snp:pileup_variants (16)
[b2/c39edf] Submitted process > snp:pileup_variants (15)
[9e/04269d] Submitted process > snp:pileup_variants (5)
[af/4d2611] Submitted process > snp:pileup_variants (8)
[ea/0519fa] Submitted process > snp:pileup_variants (17)
[07/cb8d7f] Submitted process > snp:pileup_variants (2)
[5f/24e38d] Submitted process > snp:pileup_variants (12)
[f9/32ec82] Submitted process > snp:pileup_variants (14)
[27/eb11f8] Submitted process > snp:pileup_variants (1)
[81/16c994] Submitted process > snp:pileup_variants (19)
[18/8dee10] Submitted process > snp:pileup_variants (10)
[d5/c7c5d8] Submitted process > snp:pileup_variants (4)
[5b/ee3d6a] Submitted process > snp:pileup_variants (20)
[ab/c84499] Submitted process > snp:pileup_variants (26)
[db/31b41d] Submitted process > snp:pileup_variants (24)
[64/c62b1d] Submitted process > snp:pileup_variants (21)
[e4/dc8878] Submitted process > snp:pileup_variants (23)
[53/dc7ee0] Submitted process > snp:pileup_variants (22)
[2d/5d0b92] Submitted process > snp:pileup_variants (28)
[5b/426f14] Submitted process > snp:pileup_variants (27)
[6f/4c21f2] Submitted process > snp:pileup_variants (25)
[f9/1cdf3a] Submitted process > snp:pileup_variants (33)
[f2/fc36ae] Submitted process > snp:pileup_variants (36)
[32/ce2e75] Submitted process > snp:pileup_variants (29)
[6b/2a70f5] Submitted process > snp:pileup_variants (37)
[13/b903e5] Submitted process > snp:pileup_variants (32)
[35/b5aaf6] Submitted process > snp:pileup_variants (38)
[31/a2762d] Submitted process > snp:pileup_variants (35)
[d0/a0e8ab] Submitted process > snp:pileup_variants (34)
[39/3c7d79] Submitted process > snp:pileup_variants (30)
[2b/1086da] Submitted process > snp:pileup_variants (31)
[01/d28a8a] Submitted process > snp:pileup_variants (41)
[da/fe5c8a] Submitted process > snp:pileup_variants (40)
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[2b/e2e693] Submitted process > snp:pileup_variants (47)
[27/31f006] Submitted process > snp:pileup_variants (45)
[2d/5af6e2] Submitted process > snp:pileup_variants (46)
[c2/7eeb96] Submitted process > snp:pileup_variants (42)
[b1/6d57f3] Submitted process > snp:pileup_variants (48)
[2a/3724a4] Submitted process > snp:pileup_variants (43)
[4e/5294e5] Submitted process > snp:pileup_variants (52)
[d9/199e04] Submitted process > snp:pileup_variants (49)
[82/786c3b] Submitted process > snp:pileup_variants (53)
[d1/b57e12] Submitted process > snp:pileup_variants (56)
[08/622b40] Submitted process > snp:pileup_variants (51)
[49/f12935] Submitted process > snp:pileup_variants (50)
[94/b248ec] Submitted process > snp:pileup_variants (55)
[e9/d8a400] Submitted process > snp:pileup_variants (54)
[01/b96673] Submitted process > snp:pileup_variants (57)
[70/bf4f2c] Submitted process > snp:pileup_variants (65)
[cb/e80eb7] Submitted process > snp:pileup_variants (64)
[6c/f38546] Submitted process > snp:pileup_variants (60)
[e8/324c1b] Submitted process > snp:pileup_variants (61)
[74/4b8794] Submitted process > snp:pileup_variants (58)
[f8/19c091] Submitted process > snp:pileup_variants (62)
[07/cd3cc7] Submitted process > snp:pileup_variants (63)
[d5/d4724a] Submitted process > snp:pileup_variants (70)
[3a/2fe84c] Submitted process > snp:pileup_variants (69)
[9e/c56aab] Submitted process > snp:pileup_variants (67)
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[0a/1efe54] Submitted process > snp:pileup_variants (73)
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[ca/eae746] Submitted process > snp:pileup_variants (75)
[2f/2e32e0] Submitted process > snp:pileup_variants (71)
[69/d95b20] Submitted process > snp:pileup_variants (74)
[fd/67cbfe] Submitted process > snp:pileup_variants (78)
[08/9b60e0] Submitted process > snp:pileup_variants (76)
[ab/6b519d] Submitted process > snp:pileup_variants (80)
[5e/5b0c81] Submitted process > snp:pileup_variants (81)
[a4/e439a7] Submitted process > snp:pileup_variants (77)
[5e/563050] Submitted process > snp:pileup_variants (82)
[7d/9d7cf9] Submitted process > snp:pileup_variants (79)
[51/0c2325] Submitted process > snp:pileup_variants (89)
[6f/83208b] Submitted process > snp:pileup_variants (90)
[10/20968f] Submitted process > snp:pileup_variants (86)
[d4/3d0ad4] Submitted process > snp:pileup_variants (88)
[3c/183a64] Submitted process > snp:pileup_variants (84)
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[27/5f1403] Submitted process > snp:pileup_variants (85)
[7b/402497] Submitted process > snp:pileup_variants (91)
[4d/34672c] Submitted process > snp:pileup_variants (87)
[18/ccd4e8] Submitted process > snp:pileup_variants (93)
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[56/aa8cab] Submitted process > snp:pileup_variants (95)
[a0/9049d3] Submitted process > snp:pileup_variants (94)
[41/ebcd71] Submitted process > snp:pileup_variants (98)
[d8/65a5b1] Submitted process > snp:pileup_variants (97)
[cd/c04428] Submitted process > snp:pileup_variants (100)
[86/220a04] Submitted process > snp:pileup_variants (96)
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[b4/39dd39] Submitted process > snp:pileup_variants (103)
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[8e/54633d] Submitted process > snp:pileup_variants (124)
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[2b/371b13] Submitted process > snp:pileup_variants (117)
[ca/41e5d9] Submitted process > snp:pileup_variants (121)
[54/74e1ca] Submitted process > snp:pileup_variants (119)
[b7/705918] Submitted process > snp:pileup_variants (123)
[6e/1a3578] Submitted process > snp:pileup_variants (120)
[73/b1ceb1] Submitted process > snp:pileup_variants (118)
[00/c99151] Submitted process > snp:pileup_variants (116)
[9d/bad27b] Submitted process > snp:pileup_variants (122)
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[d0/1d38fe] Submitted process > snp:pileup_variants (128)
[54/322257] Submitted process > snp:pileup_variants (130)
[a9/fcec95] Submitted process > snp:pileup_variants (127)
[5b/f462b4] Submitted process > snp:pileup_variants (129)
[9e/e8797a] Submitted process > snp:pileup_variants (134)
[a8/40b45e] Submitted process > snp:pileup_variants (133)
[30/a5575e] Submitted process > snp:pileup_variants (132)
[c6/df24de] Submitted process > snp:pileup_variants (135)
[21/f1d102] Submitted process > snp:pileup_variants (131)
[26/b14baf] Submitted process > snp:pileup_variants (138)
[31/58a52e] Submitted process > snp:pileup_variants (142)
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[f9/625436] Submitted process > snp:pileup_variants (137)
[6f/1bd7d6] Submitted process > snp:pileup_variants (144)
[5c/5fd03b] Submitted process > snp:pileup_variants (143)
[df/073a2b] Submitted process > snp:pileup_variants (145)
[bd/7b0b32] Submitted process > snp:pileup_variants (146)
[92/8e6101] Submitted process > snp:pileup_variants (136)
[1f/458bf1] Submitted process > snp:pileup_variants (141)
[eb/6ab419] Submitted process > snp:pileup_variants (147)
[dc/af7c49] Submitted process > snp:pileup_variants (139)
[07/58193e] Submitted process > snp:pileup_variants (149)
[0a/7f5377] Submitted process > snp:pileup_variants (152)
[d5/2679f1] Submitted process > snp:pileup_variants (148)
[36/ca865e] Submitted process > snp:pileup_variants (151)
[18/d9db29] Submitted process > snp:pileup_variants (159)
[4e/61f860] Submitted process > snp:pileup_variants (153)
[50/903af9] Submitted process > snp:pileup_variants (156)
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[8f/8b3037] Submitted process > snp:pileup_variants (158)
[ed/0beb1e] Submitted process > snp:pileup_variants (150)
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[5d/012d2d] Submitted process > snp:pileup_variants (157)
[f7/b3d966] Submitted process > snp:pileup_variants (169)
[18/d723f9] Submitted process > snp:pileup_variants (165)
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[c2/6a8e32] Submitted process > snp:pileup_variants (161)
[35/b22e7e] Submitted process > snp:pileup_variants (168)
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[27/fb410a] Submitted process > snp:pileup_variants (256)
[3e/8defec] Submitted process > snp:pileup_variants (257)
[50/f82ec4] Submitted process > snp:pileup_variants (258)
[3f/7686bb] Submitted process > snp:pileup_variants (260)
[97/8e9dd0] Submitted process > snp:pileup_variants (259)
[e5/e039d1] Submitted process > snp:pileup_variants (255)
[5f/21acaa] Submitted process > snp:pileup_variants (262)
[5a/613ffe] Submitted process > snp:pileup_variants (261)
[b2/b37adc] Submitted process > snp:pileup_variants (265)
[33/0df2b7] Submitted process > snp:pileup_variants (264)
[62/69343c] Submitted process > snp:pileup_variants (266)
[68/209e19] Submitted process > snp:pileup_variants (268)
[26/a35417] Submitted process > snp:pileup_variants (272)
[0f/b40aeb] Submitted process > snp:pileup_variants (269)
[f1/83e6f8] Submitted process > snp:pileup_variants (270)
[d3/8d6e41] Submitted process > snp:pileup_variants (267)
[43/690086] Submitted process > snp:pileup_variants (263)
[46/39cfc7] Submitted process > snp:pileup_variants (271)
[a4/38e31b] Submitted process > snp:pileup_variants (274)
[c7/b82d25] Submitted process > snp:pileup_variants (277)
[d4/b46ff1] Submitted process > snp:pileup_variants (273)
[ad/82c65c] Submitted process > snp:pileup_variants (283)
[51/b62c0b] Submitted process > snp:pileup_variants (275)
[3c/8da7aa] Submitted process > snp:pileup_variants (276)
[da/e4910c] Submitted process > snp:pileup_variants (282)
[07/12060e] Submitted process > snp:pileup_variants (284)
[a4/fae2c5] Submitted process > snp:pileup_variants (279)
[f8/81629f] Submitted process > snp:pileup_variants (278)
[7e/31cdf5] Submitted process > snp:pileup_variants (280)
[c2/894e74] Submitted process > snp:pileup_variants (281)
[0a/5d58f8] Submitted process > snp:pileup_variants (286)
[28/980331] Submitted process > snp:pileup_variants (288)
[67/590724] Submitted process > snp:pileup_variants (291)
[17/4bf02c] Submitted process > snp:pileup_variants (289)
[14/831760] Submitted process > snp:pileup_variants (290)
[12/170817] Submitted process > snp:pileup_variants (287)
[85/e20517] Submitted process > snp:pileup_variants (285)
[48/50ba34] Submitted process > snp:pileup_variants (302)
[5e/870910] Submitted process > snp:pileup_variants (300)
[9d/e1936b] Submitted process > snp:pileup_variants (299)
[d2/c7a817] Submitted process > snp:pileup_variants (304)
[07/4beec5] Submitted process > snp:pileup_variants (301)
[cf/6d5d15] Submitted process > snp:pileup_variants (296)
[58/a152d6] Submitted process > snp:pileup_variants (294)
[d0/89b2de] Submitted process > snp:pileup_variants (303)
[80/6a9eae] Submitted process > snp:pileup_variants (298)
[9f/1e5a70] Submitted process > snp:pileup_variants (293)
[0f/de89f1] Submitted process > snp:pileup_variants (297)
[bc/d07112] Submitted process > snp:pileup_variants (292)
[1a/0ac940] Submitted process > snp:pileup_variants (310)
[5a/3c9e35] Submitted process > snp:pileup_variants (308)
[5b/0430a1] Submitted process > snp:pileup_variants (307)
[91/72d563] Submitted process > snp:pileup_variants (309)
[95/5940bc] Submitted process > snp:pileup_variants (305)
[b0/7d1bba] Submitted process > snp:pileup_variants (306)
[a1/2b970b] Submitted process > snp:pileup_variants (295)
[0a/89752d] Submitted process > snp:pileup_variants (319)
[8a/19715b] Submitted process > snp:pileup_variants (321)
[1a/09b82c] Submitted process > snp:pileup_variants (311)
[8f/9ac341] Submitted process > snp:pileup_variants (312)
[23/de6009] Submitted process > snp:pileup_variants (315)
[fd/e1e3b6] Submitted process > snp:pileup_variants (323)
[62/a47d4b] Submitted process > snp:pileup_variants (317)
[ee/fd76f0] Submitted process > snp:pileup_variants (320)
[1a/fd4baa] Submitted process > snp:pileup_variants (325)
[ce/f851fc] Submitted process > snp:pileup_variants (324)
[0d/c7cb1d] Submitted process > snp:pileup_variants (318)
[51/ccae59] Submitted process > snp:pileup_variants (326)
[3c/867ffd] Submitted process > snp:pileup_variants (313)
[f0/6a669d] Submitted process > snp:pileup_variants (322)
[ea/0342ea] Submitted process > snp:pileup_variants (328)
[38/7f9f25] Submitted process > snp:pileup_variants (316)
[9d/e373e7] Submitted process > snp:pileup_variants (331)
[4f/bcbe5e] Submitted process > snp:pileup_variants (329)
[8d/0494ee] Submitted process > snp:pileup_variants (314)
[46/54b318] Submitted process > snp:pileup_variants (327)
[f4/29740d] Submitted process > snp:pileup_variants (337)
[aa/7bbfcb] Submitted process > snp:pileup_variants (341)
[0c/457209] Submitted process > snp:pileup_variants (333)
[86/d6dcf1] Submitted process > snp:pileup_variants (334)
[3e/51b777] Submitted process > snp:pileup_variants (344)
[e4/988157] Submitted process > snp:pileup_variants (330)
[bc/a493a8] Submitted process > snp:pileup_variants (336)
[56/d9a722] Submitted process > snp:pileup_variants (338)
[a8/ab1c70] Submitted process > snp:pileup_variants (335)
[8e/e34343] Submitted process > snp:pileup_variants (339)
[6c/9e3f93] Submitted process > snp:pileup_variants (332)
[ea/c355f2] Submitted process > snp:pileup_variants (342)
[19/ad825f] Submitted process > snp:pileup_variants (340)
[a4/3dea52] Submitted process > snp:pileup_variants (343)
[c2/359f65] Submitted process > snp:pileup_variants (347)
[1c/ce03b7] Submitted process > snp:pileup_variants (349)
[69/b5f80f] Submitted process > snp:pileup_variants (345)
[f5/b54268] Submitted process > snp:pileup_variants (346)
[77/032e91] Submitted process > snp:pileup_variants (348)
[84/7edb0d] Submitted process > snp:pileup_variants (350)
[10/2a43f3] Submitted process > snp:pileup_variants (358)
[2d/438e3b] Submitted process > snp:pileup_variants (351)
[6f/2d55d3] Submitted process > snp:pileup_variants (353)
[0f/59a606] Submitted process > snp:pileup_variants (354)
[a7/24c029] Submitted process > snp:pileup_variants (357)
[34/05c732] Submitted process > snp:pileup_variants (352)
[a1/5df9f4] Submitted process > snp:pileup_variants (359)
[b5/ae65a2] Submitted process > snp:pileup_variants (355)
[ae/e74818] Submitted process > snp:pileup_variants (356)
[b2/5a5862] Submitted process > snp:pileup_variants (361)
[9a/fc0901] Submitted process > snp:pileup_variants (367)
[7b/6faadd] Submitted process > snp:pileup_variants (360)
[b3/cfa094] Submitted process > snp:pileup_variants (363)
[3b/5b088b] Submitted process > snp:pileup_variants (366)
[02/d5895f] Submitted process > snp:pileup_variants (362)
[75/4cdc74] Submitted process > snp:pileup_variants (369)
[04/56575a] Submitted process > snp:pileup_variants (368)
[5f/7fcdd0] Submitted process > snp:pileup_variants (376)
[29/d9a700] Submitted process > snp:pileup_variants (365)
[b7/9c3add] Submitted process > snp:pileup_variants (374)
[07/d2eadc] Submitted process > snp:pileup_variants (372)
[23/f03336] Submitted process > snp:pileup_variants (371)
[ac/b333a0] Submitted process > snp:pileup_variants (370)
[e2/7ef144] Submitted process > snp:pileup_variants (375)
[09/3b9a29] Submitted process > snp:pileup_variants (364)
[11/0f938c] Submitted process > snp:pileup_variants (373)
[9a/0e7a97] Submitted process > snp:pileup_variants (378)
[3e/0adfab] Submitted process > snp:pileup_variants (382)
[1c/736e42] Submitted process > snp:pileup_variants (380)
[71/736eed] Submitted process > snp:pileup_variants (381)
[7b/63ed90] Submitted process > snp:pileup_variants (379)
[f7/c76eee] Submitted process > snp:pileup_variants (393)
[1a/ac5df2] Submitted process > snp:pileup_variants (377)
[d7/57260d] Submitted process > snp:pileup_variants (391)
[56/f63146] Submitted process > snp:pileup_variants (384)
[5c/1f0719] Submitted process > snp:pileup_variants (388)
[b7/d194c9] Submitted process > snp:pileup_variants (385)
[37/7b33cb] Submitted process > snp:pileup_variants (390)
[c5/eda6dd] Submitted process > snp:pileup_variants (383)
[25/8ad939] Submitted process > snp:pileup_variants (387)
[14/ff21a2] Submitted process > snp:pileup_variants (392)
[d7/b48b2a] Submitted process > snp:pileup_variants (386)
[c6/aa6699] Submitted process > snp:pileup_variants (389)
[c1/e1b489] Submitted process > snp:pileup_variants (394)
[71/364e9a] Submitted process > snp:pileup_variants (396)
[fc/6c2d14] Submitted process > snp:pileup_variants (395)
[a9/1e8fef] Submitted process > snp:pileup_variants (399)
[62/1a2a7d] Submitted process > snp:pileup_variants (397)
[ec/d912c3] Submitted process > snp:pileup_variants (400)
[6a/678551] Submitted process > snp:pileup_variants (398)
[ad/9ee1e2] Submitted process > snp:pileup_variants (401)
[89/399abd] Submitted process > snp:pileup_variants (403)
[95/429903] Submitted process > snp:pileup_variants (402)
[59/76aa18] Submitted process > snp:pileup_variants (404)
[e2/5ba972] Submitted process > snp:pileup_variants (405)
[b5/896839] Submitted process > snp:pileup_variants (409)
[19/f301bb] Submitted process > snp:pileup_variants (408)
[d1/4da700] Submitted process > snp:pileup_variants (407)
[22/7d4ff9] Submitted process > snp:pileup_variants (413)
[4c/1b232b] Submitted process > snp:pileup_variants (414)
[c8/a91d52] Submitted process > snp:pileup_variants (406)
[ee/eb0c92] Submitted process > snp:pileup_variants (410)
[c8/437870] Submitted process > snp:pileup_variants (417)
[a7/a3311e] Submitted process > snp:pileup_variants (412)
[0b/ede743] Submitted process > snp:pileup_variants (411)
[7f/6954ec] Submitted process > snp:pileup_variants (419)
[07/d31ac8] Submitted process > snp:pileup_variants (418)
[5e/a2a5e4] Submitted process > snp:pileup_variants (416)
[20/69e2b7] Submitted process > snp:pileup_variants (415)
[bf/08d345] Submitted process > snp:pileup_variants (423)
[aa/67f4d4] Submitted process > snp:pileup_variants (432)
[bf/d492c8] Submitted process > snp:pileup_variants (420)
[dd/cb9c7b] Submitted process > snp:pileup_variants (427)
[44/38745b] Submitted process > snp:pileup_variants (434)
[9f/306aa1] Submitted process > snp:pileup_variants (424)
[54/13d7fd] Submitted process > snp:pileup_variants (428)
[6a/1a9158] Submitted process > snp:pileup_variants (421)
[df/07c654] Submitted process > snp:pileup_variants (425)
[f1/07d014] Submitted process > snp:pileup_variants (431)
[bf/f94ccd] Submitted process > snp:pileup_variants (422)
[08/d581f3] Submitted process > snp:pileup_variants (426)
[90/7d9412] Submitted process > snp:pileup_variants (430)
[a5/f7d7bc] Submitted process > snp:pileup_variants (433)
[44/1c2594] Submitted process > snp:pileup_variants (429)
[8e/4a6d94] Submitted process > snp:pileup_variants (438)
[67/cee899] Submitted process > snp:pileup_variants (435)
[85/3e8031] Submitted process > snp:pileup_variants (440)
[ec/4910e0] Submitted process > snp:pileup_variants (436)
[7d/1a0d32] Submitted process > snp:pileup_variants (442)
[07/cffc61] Submitted process > snp:pileup_variants (447)
[5f/07469d] Submitted process > snp:pileup_variants (437)
[73/a86a18] Submitted process > snp:pileup_variants (443)
[7b/51bbaf] Submitted process > snp:pileup_variants (439)
[69/c62af8] Submitted process > snp:pileup_variants (444)
[d6/f00902] Submitted process > snp:pileup_variants (445)
[ee/8d0ded] Submitted process > snp:pileup_variants (446)
[86/109c12] Submitted process > snp:pileup_variants (441)
[56/9777f1] Submitted process > snp:pileup_variants (448)
[4e/869a41] Submitted process > snp:pileup_variants (451)
[b5/b91ca3] Submitted process > snp:pileup_variants (456)
[8d/36a190] Submitted process > snp:pileup_variants (453)
[59/1b35f4] Submitted process > snp:pileup_variants (450)
[39/6e52eb] Submitted process > snp:pileup_variants (452)
[3d/8e4faf] Submitted process > snp:pileup_variants (454)
[15/e3689f] Submitted process > snp:pileup_variants (449)
[47/02db0c] Submitted process > snp:pileup_variants (455)
[f7/337d80] Submitted process > snp:pileup_variants (471)
[90/10485c] Submitted process > snp:pileup_variants (470)
[6e/834e14] Submitted process > snp:pileup_variants (464)
[37/37b9f3] Submitted process > snp:pileup_variants (459)
[c5/51e00a] Submitted process > snp:pileup_variants (466)
[c2/00d0a8] Submitted process > snp:pileup_variants (461)
[7c/c5f854] Submitted process > snp:pileup_variants (467)
[c6/eec9a4] Submitted process > snp:pileup_variants (460)
[5d/3dbbde] Submitted process > snp:pileup_variants (472)
[da/958a8b] Submitted process > snp:pileup_variants (462)
[c9/cf74b9] Submitted process > snp:pileup_variants (469)
[bb/012eab] Submitted process > snp:pileup_variants (458)
[cd/624385] Submitted process > snp:pileup_variants (465)
[f1/a5b327] Submitted process > snp:pileup_variants (468)
[48/d4fac8] Submitted process > snp:pileup_variants (463)
[f9/59a66a] Submitted process > snp:pileup_variants (457)
[a4/ff850b] Submitted process > snp:pileup_variants (473)
[85/f73b6e] Submitted process > snp:pileup_variants (475)
[50/0eec8b] Submitted process > snp:pileup_variants (474)
[e8/534ea9] Submitted process > snp:pileup_variants (476)
[63/e2d8e1] Submitted process > snp:pileup_variants (479)
[a5/112803] Submitted process > snp:pileup_variants (482)
[8f/4b1a4c] Submitted process > snp:pileup_variants (483)
[40/0ea4c3] Submitted process > snp:pileup_variants (489)
[29/eef148] Submitted process > snp:pileup_variants (486)
[4d/d6bd9e] Submitted process > snp:pileup_variants (485)
[c5/7fc4b4] Submitted process > snp:pileup_variants (487)
[5c/93dba0] Submitted process > snp:pileup_variants (480)
[73/2fe9af] Submitted process > snp:pileup_variants (490)
[a9/beaa49] Submitted process > snp:pileup_variants (491)
[82/35af20] Submitted process > snp:pileup_variants (492)
[42/98b730] Submitted process > snp:pileup_variants (477)
[7a/bd50db] Submitted process > snp:pileup_variants (493)
[e9/70d3d7] Submitted process > snp:pileup_variants (484)
[57/e69ad6] Submitted process > snp:pileup_variants (478)
[06/455148] Submitted process > snp:pileup_variants (488)
[77/29deec] Submitted process > snp:pileup_variants (481)
[bd/c14e3e] Submitted process > snp:pileup_variants (494)
[39/03ec4a] Submitted process > snp:pileup_variants (501)
[39/227ab8] Submitted process > snp:pileup_variants (499)
[20/45cfda] Submitted process > snp:pileup_variants (509)
[b6/23e504] Submitted process > snp:pileup_variants (508)
[87/3b57df] Submitted process > snp:pileup_variants (495)
[09/93aed2] Submitted process > snp:pileup_variants (498)
[ee/2701f7] Submitted process > snp:pileup_variants (506)
[52/d8b30b] Submitted process > snp:pileup_variants (505)
[fd/9ec742] Submitted process > snp:pileup_variants (500)
[4a/578e39] Submitted process > snp:pileup_variants (507)
[d5/c00ea7] Submitted process > snp:pileup_variants (503)
[a2/37b6d8] Submitted process > snp:pileup_variants (496)
[55/292bcb] Submitted process > snp:pileup_variants (502)
[2e/2e5966] Submitted process > snp:pileup_variants (504)
[33/da45c1] Submitted process > snp:pileup_variants (497)
[74/ed588d] Submitted process > snp:pileup_variants (512)
[b9/2dcf7e] Submitted process > snp:pileup_variants (511)
[fb/0d16fe] Submitted process > snp:pileup_variants (510)
[81/1e742d] Submitted process > snp:pileup_variants (527)
[31/fd4c4d] Submitted process > snp:pileup_variants (522)
[dd/712831] Submitted process > snp:pileup_variants (529)
[4d/d543d4] Submitted process > snp:pileup_variants (518)
[f2/5ddb19] Submitted process > snp:pileup_variants (521)
[89/823245] Submitted process > snp:pileup_variants (513)
[b3/75b905] Submitted process > snp:pileup_variants (515)
[27/efefe9] Submitted process > snp:pileup_variants (526)
[3e/abedd8] Submitted process > snp:pileup_variants (520)
[2a/cba61b] Submitted process > snp:pileup_variants (516)
[5f/6cbce5] Submitted process > snp:pileup_variants (528)
[e1/9dfc1c] Submitted process > snp:pileup_variants (517)
[b9/678b86] Submitted process > snp:pileup_variants (525)
[26/212b2f] Submitted process > snp:pileup_variants (540)
[8f/057a99] Submitted process > snp:pileup_variants (524)
[f7/985b10] Submitted process > snp:pileup_variants (531)
[a8/bdb096] Submitted process > snp:pileup_variants (532)
[0e/fc4ebe] Submitted process > snp:pileup_variants (514)
[13/68b2dd] Submitted process > snp:pileup_variants (541)
[5f/752de7] Submitted process > snp:pileup_variants (534)
[f9/19b0d8] Submitted process > snp:pileup_variants (536)
[3b/7ba0c6] Submitted process > snp:pileup_variants (542)
[d4/7b9222] Submitted process > snp:pileup_variants (539)
[83/fe96e9] Submitted process > snp:pileup_variants (523)
[42/ca0049] Submitted process > snp:pileup_variants (538)
[c6/c86743] Submitted process > snp:pileup_variants (537)
[36/cb06e5] Submitted process > snp:pileup_variants (535)
[9e/8439c9] Submitted process > snp:pileup_variants (533)
[5b/765ebc] Submitted process > snp:pileup_variants (543)
[27/7ce75c] Submitted process > snp:pileup_variants (530)
[6e/795007] Submitted process > snp:pileup_variants (544)
[a6/c3e42c] Submitted process > snp:pileup_variants (519)
[1e/75a995] Submitted process > snp:pileup_variants (545)
[f2/c23943] Submitted process > snp:pileup_variants (547)
[1f/a29057] Submitted process > snp:pileup_variants (550)
[f4/01a4a7] Submitted process > snp:pileup_variants (554)
[90/2974da] Submitted process > snp:pileup_variants (562)
[8f/9f4913] Submitted process > snp:pileup_variants (552)
[27/ba9038] Submitted process > snp:pileup_variants (555)
[d3/0831c0] Submitted process > snp:pileup_variants (561)
[e1/480f22] Submitted process > snp:pileup_variants (556)
[20/c97acb] Submitted process > snp:pileup_variants (551)
[6d/6b6019] Submitted process > snp:pileup_variants (553)
[54/313ad6] Submitted process > snp:pileup_variants (549)
[35/9b21ec] Submitted process > snp:pileup_variants (559)
[f8/172a27] Submitted process > snp:pileup_variants (557)
[be/bf19d8] Submitted process > snp:pileup_variants (548)
[ba/c57dc1] Submitted process > snp:pileup_variants (558)
[5f/50026d] Submitted process > snp:pileup_variants (560)
[e0/1602fe] Submitted process > snp:pileup_variants (546)
[11/c10dae] Submitted process > snp:pileup_variants (563)
[af/25a7f1] Submitted process > snp:pileup_variants (570)
[eb/6284da] Submitted process > snp:pileup_variants (573)
[50/07f87f] Submitted process > snp:pileup_variants (567)
[e4/3cdfa1] Submitted process > snp:pileup_variants (575)
[0b/383319] Submitted process > snp:pileup_variants (577)
[99/93bc71] Submitted process > snp:pileup_variants (568)
[0f/9db596] Submitted process > snp:pileup_variants (564)
[29/7acc97] Submitted process > snp:pileup_variants (576)
[a0/871c5a] Submitted process > snp:pileup_variants (574)
[17/7c5906] Submitted process > snp:pileup_variants (571)
[94/f9dafb] Submitted process > snp:pileup_variants (565)
[53/8e55a6] Submitted process > snp:pileup_variants (578)
[d0/98508d] Submitted process > snp:pileup_variants (579)
[35/2e1d84] Submitted process > snp:pileup_variants (566)
[fb/0f7831] Submitted process > snp:pileup_variants (580)
[ea/41bca2] Submitted process > snp:pileup_variants (569)
[12/23760c] Submitted process > snp:pileup_variants (572)
[4a/a80172] Submitted process > snp:pileup_variants (582)
[bc/14a943] Submitted process > snp:pileup_variants (581)
[03/3cd810] Submitted process > snp:pileup_variants (587)
[9f/cbd0bb] Submitted process > snp:pileup_variants (592)
[95/358f1a] Submitted process > snp:pileup_variants (598)
[7a/72191f] Submitted process > snp:pileup_variants (585)
[42/cf315f] Submitted process > snp:pileup_variants (584)
[91/aea82e] Submitted process > snp:pileup_variants (586)
[3a/0f7a5f] Submitted process > snp:pileup_variants (597)
[ce/7896cd] Submitted process > snp:pileup_variants (590)
[c8/fff489] Submitted process > snp:pileup_variants (599)
[df/3b897c] Submitted process > snp:pileup_variants (589)
[04/b3c81b] Submitted process > snp:pileup_variants (588)
[3c/21c6de] Submitted process > snp:pileup_variants (594)
[64/8d3f05] Submitted process > snp:pileup_variants (591)
[31/31618c] Submitted process > snp:pileup_variants (595)
[03/836d26] Submitted process > snp:pileup_variants (583)
[dc/5c5f1e] Submitted process > snp:pileup_variants (593)
[87/1442c8] Submitted process > snp:pileup_variants (596)
[cb/b4df44] Submitted process > snp:pileup_variants (600)
[87/0b29b9] Submitted process > snp:pileup_variants (602)
[52/85ffe5] Submitted process > snp:pileup_variants (608)
[fc/108d53] Submitted process > snp:pileup_variants (612)
[07/86f373] Submitted process > snp:pileup_variants (606)
[b8/81f7c6] Submitted process > snp:pileup_variants (610)
[f1/942b74] Submitted process > snp:pileup_variants (611)
[8c/9c1985] Submitted process > snp:pileup_variants (613)
[28/d42cfc] Submitted process > snp:pileup_variants (604)
[98/8b6a36] Submitted process > snp:pileup_variants (605)
[4e/857f28] Submitted process > snp:pileup_variants (615)
[ac/99c4d1] Submitted process > snp:pileup_variants (607)
[4f/10ca2b] Submitted process > snp:pileup_variants (616)
[6b/2663ef] Submitted process > snp:pileup_variants (601)
[73/379ada] Submitted process > snp:pileup_variants (603)
[50/32565f] Submitted process > snp:pileup_variants (609)
[9d/f801e5] Submitted process > snp:pileup_variants (619)
[82/65b101] Submitted process > snp:pileup_variants (618)
[a2/f4732b] Submitted process > snp:pileup_variants (617)
[be/bbd6d9] Submitted process > snp:pileup_variants (614)
[ce/8bddd9] Submitted process > snp:pileup_variants (620)
[94/1deee5] Submitted process > snp:aggregate_pileup_variants (1)
[de/22c9a4] Submitted process > snp:select_het_snps (18)
[0d/64bb27] Submitted process > snp:select_het_snps (8)
[41/0c4ad2] Submitted process > snp:select_het_snps (12)
[18/dda35a] Submitted process > snp:select_het_snps (17)
[81/d7ec45] Submitted process > snp:select_het_snps (6)
[e3/3ff99b] Submitted process > snp:select_het_snps (1)
[36/75e1a8] Submitted process > snp:select_het_snps (19)
[32/c2e0b2] Submitted process > snp:select_het_snps (11)
[da/60279f] Submitted process > snp:select_het_snps (7)
[6d/202b8a] Submitted process > snp:select_het_snps (10)
[20/1feb36] Submitted process > snp:select_het_snps (5)
[ae/f82069] Submitted process > snp:select_het_snps (3)
[2e/7a554f] Submitted process > snp:select_het_snps (14)
[1c/5d4a26] Submitted process > snp:select_het_snps (15)
[e7/b1c458] Submitted process > snp:select_het_snps (2)
[49/cae10e] Submitted process > snp:select_het_snps (9)
[c0/c489cd] Submitted process > snp:select_het_snps (4)
[6d/645bf0] Submitted process > snp:select_het_snps (13)
[f8/c9494b] Submitted process > snp:select_het_snps (16)
[ab/aa4856] Submitted process > snp:select_het_snps (23)
[52/82768a] Submitted process > snp:select_het_snps (22)
[69/beaaac] Submitted process > snp:select_het_snps (21)
[66/1fcfc9] Submitted process > snp:select_het_snps (20)
[1a/e7bac6] Submitted process > snp:select_het_snps (24)
[43/988615] Submitted process > snp:get_qual_filter (1)
[4c/05ac88] Submitted process > snp:phase_contig (1)
[df/5aa0b0] Submitted process > snp:phase_contig (2)
[30/160da5] Submitted process > snp:phase_contig (3)
[56/e1dc45] Submitted process > snp:phase_contig (4)
[df/1c4f8a] Submitted process > snp:create_candidates (7)
[d5/40cbb7] Submitted process > snp:phase_contig (5)
[9d/e78afb] Submitted process > snp:phase_contig (6)
[5e/56e1fc] Submitted process > snp:phase_contig (7)
[90/b7bf90] Submitted process > snp:phase_contig (8)
[32/b2f29c] Submitted process > snp:create_candidates (5)
[fd/490dbf] Submitted process > snp:phase_contig (9)
[c8/bc20b6] Submitted process > snp:phase_contig (10)
[dd/67d990] Submitted process > snp:create_candidates (19)
[20/de4501] Submitted process > snp:phase_contig (11)
[59/ad0c50] Submitted process > snp:phase_contig (12)
[83/759eee] Submitted process > snp:phase_contig (13)
[6a/e3f65f] Submitted process > snp:phase_contig (14)
[d5/281ab9] Submitted process > snp:create_candidates (11)
[59/45d420] Submitted process > snp:phase_contig (15)
[7d/d5c999] Submitted process > snp:phase_contig (16)
[c8/319664] Submitted process > snp:phase_contig (17)
[89/66ab40] Submitted process > snp:create_candidates (14)
[77/aaeadf] Submitted process > snp:phase_contig (18)
[3a/529a26] Submitted process > snp:phase_contig (19)
[79/130b51] Submitted process > snp:create_candidates (13)
[87/10199c] Submitted process > snp:phase_contig (20)
[8d/b7c019] Submitted process > snp:phase_contig (21)
[84/b3b439] Submitted process > snp:phase_contig (22)
[9f/65a841] Submitted process > snp:phase_contig (23)
[4f/fc4857] Submitted process > snp:create_candidates (9)
[01/00eebf] Submitted process > snp:phase_contig (24)
[20/b865c5] Submitted process > snp:create_candidates (12)
[13/82762a] Submitted process > snp:create_candidates (4)
[c9/0483a9] Submitted process > snp:create_candidates (16)
[49/b3e560] Submitted process > snp:create_candidates (21)
[f7/1adc4b] Submitted process > snp:create_candidates (17)
[96/75fbc5] Submitted process > snp:create_candidates (3)
[cd/0d1c76] Submitted process > snp:create_candidates (15)
[1c/e73229] Submitted process > snp:create_candidates (1)
[32/4a606e] Submitted process > snp:create_candidates (2)
[50/4cd6d9] Submitted process > snp:create_candidates (22)
[d9/d52078] Submitted process > snp:create_candidates (8)
[c1/e58ef2] Submitted process > snp:create_candidates (18)
[64/11daa0] Submitted process > snp:create_candidates (20)
[dd/46dcc8] Submitted process > snp:create_candidates (10)
[d5/7be212] Submitted process > snp:create_candidates (6)
[1f/c7ad7e] Submitted process > snp:create_candidates (23)
[89/8b1514] Submitted process > snp:create_candidates (24)
[7e/f01841] Submitted process > snp:evaluate_candidates (3)
[c8/6e8bb4] Submitted process > snp:evaluate_candidates (7)
[97/85178d] Submitted process > snp:evaluate_candidates (6)
[99/4198c1] Submitted process > snp:evaluate_candidates (8)
[11/ce48dd] Submitted process > snp:evaluate_candidates (5)
[e8/32d24d] Submitted process > snp:evaluate_candidates (1)
[42/25691c] Submitted process > snp:evaluate_candidates (4)
[35/77df40] Submitted process > snp:evaluate_candidates (10)
[3c/1d69c8] Submitted process > snp:evaluate_candidates (2)
[ee/360f36] Submitted process > snp:evaluate_candidates (9)
[20/707577] Submitted process > snp:evaluate_candidates (17)
[b8/226818] Submitted process > snp:evaluate_candidates (13)
[7c/1d8968] Submitted process > snp:evaluate_candidates (14)
[3c/13e497] Submitted process > snp:evaluate_candidates (16)
[d1/89ec2f] Submitted process > snp:evaluate_candidates (11)
[3f/107f91] Submitted process > snp:evaluate_candidates (12)
[9f/78e763] Submitted process > snp:evaluate_candidates (15)
[47/dcfcdf] Submitted process > snp:evaluate_candidates (20)
[7c/f5c79f] Submitted process > snp:evaluate_candidates (18)
[0e/0d6966] Submitted process > snp:evaluate_candidates (19)
[e4/54dc25] Submitted process > snp:evaluate_candidates (22)
[86/e9994d] Submitted process > snp:evaluate_candidates (23)
[3d/36eae5] Submitted process > snp:evaluate_candidates (21)
[e4/aaf896] Submitted process > snp:evaluate_candidates (24)
[55/b1bcc8] Submitted process > snp:evaluate_candidates (25)
[31/18d147] Submitted process > snp:evaluate_candidates (26)
[b4/67f7ff] Submitted process > snp:evaluate_candidates (29)
[3d/28c5f5] Submitted process > snp:evaluate_candidates (27)
[a2/0fcb2a] Submitted process > snp:evaluate_candidates (28)
[ce/4fa9b4] Submitted process > snp:evaluate_candidates (31)
[f0/741699] Submitted process > snp:evaluate_candidates (33)
[56/a5e4bb] Submitted process > snp:evaluate_candidates (30)
[47/d68fd0] Submitted process > snp:evaluate_candidates (32)
[30/17c247] Submitted process > snp:evaluate_candidates (34)
[4f/850d2a] Submitted process > snp:evaluate_candidates (36)
[24/fe37c5] Submitted process > snp:evaluate_candidates (35)
[7c/78768d] Submitted process > snp:evaluate_candidates (37)
[1e/cd1941] Submitted process > snp:evaluate_candidates (39)
[a6/5275c0] Submitted process > snp:evaluate_candidates (38)
[af/6cb387] Submitted process > snp:evaluate_candidates (40)
[c2/5a90f4] Submitted process > snp:evaluate_candidates (43)
[75/f6fb89] Submitted process > snp:evaluate_candidates (41)
[87/3be846] Submitted process > snp:evaluate_candidates (42)
[99/6a1f14] Submitted process > snp:evaluate_candidates (44)
[b7/e63256] Submitted process > snp:evaluate_candidates (45)
[03/5fb78f] Submitted process > snp:evaluate_candidates (46)
[57/c52faf] Submitted process > snp:evaluate_candidates (47)
[2c/54af6b] Submitted process > snp:evaluate_candidates (50)
[77/6a17c6] Submitted process > snp:evaluate_candidates (51)
[57/fe4cfc] Submitted process > snp:evaluate_candidates (49)
[85/9aaf13] Submitted process > snp:evaluate_candidates (48)
[45/fa0c59] Submitted process > snp:evaluate_candidates (52)
[c5/a52b1e] Submitted process > snp:evaluate_candidates (58)
[a6/67cf63] Submitted process > snp:evaluate_candidates (53)
[07/56d87c] Submitted process > snp:evaluate_candidates (54)
[51/39ac34] Submitted process > snp:evaluate_candidates (57)
[cf/70e599] Submitted process > snp:evaluate_candidates (55)
[ab/7a7e0e] Submitted process > snp:evaluate_candidates (56)
[5c/f0ec05] Submitted process > snp:evaluate_candidates (62)
[9a/37fa0e] Submitted process > snp:evaluate_candidates (59)
[af/dd0098] Submitted process > snp:evaluate_candidates (61)
[fd/c06d8c] Submitted process > snp:evaluate_candidates (60)
[3b/3891fc] Submitted process > snp:evaluate_candidates (63)
[d4/1d12a0] Submitted process > snp:evaluate_candidates (64)
[22/8aee66] Submitted process > snp:evaluate_candidates (65)
[28/b21d02] Submitted process > snp:evaluate_candidates (66)
[90/b4fac5] Submitted process > snp:evaluate_candidates (67)
[d3/d93923] Submitted process > snp:evaluate_candidates (68)
[26/5ae8d1] Submitted process > snp:evaluate_candidates (70)
[0f/1afac6] Submitted process > snp:evaluate_candidates (69)
[5f/3cb2b4] Submitted process > snp:evaluate_candidates (71)
[9e/e042b2] Submitted process > snp:evaluate_candidates (72)
[40/fc7a17] Submitted process > snp:evaluate_candidates (74)
[d5/a67718] Submitted process > snp:evaluate_candidates (75)
[41/60a6b4] Submitted process > snp:evaluate_candidates (76)
[7a/e5f586] Submitted process > snp:evaluate_candidates (73)
[2d/7cb7b0] Submitted process > snp:evaluate_candidates (80)
[66/3b3db4] Submitted process > snp:evaluate_candidates (79)
[9a/453a3e] Submitted process > snp:evaluate_candidates (77)
[6e/6a6ec7] Submitted process > snp:evaluate_candidates (78)
[47/b41e38] Submitted process > snp:evaluate_candidates (81)
[ae/50becb] Submitted process > snp:evaluate_candidates (82)
[19/f2703f] Submitted process > snp:aggregate_full_align_variants (1)
[3f/f4b90f] Submitted process > snp:merge_pileup_and_full_vars (1)
[3b/453d4a] Submitted process > snp:merge_pileup_and_full_vars (15)
[9f/50af3b] Submitted process > snp:merge_pileup_and_full_vars (13)
[73/f5288a] Submitted process > snp:merge_pileup_and_full_vars (16)
[ff/ad0113] Submitted process > snp:merge_pileup_and_full_vars (12)
[f4/752c65] Submitted process > snp:merge_pileup_and_full_vars (14)
[22/367741] Submitted process > snp:merge_pileup_and_full_vars (18)
[9e/17ba80] Submitted process > snp:merge_pileup_and_full_vars (6)
[63/cd84f5] Submitted process > snp:merge_pileup_and_full_vars (10)
[30/c8a235] Submitted process > snp:merge_pileup_and_full_vars (11)
[69/55dc62] Submitted process > snp:merge_pileup_and_full_vars (3)
[01/24169d] Submitted process > snp:merge_pileup_and_full_vars (4)
[5d/c2b4e7] Submitted process > snp:merge_pileup_and_full_vars (2)
[b6/510c04] Submitted process > snp:merge_pileup_and_full_vars (7)
[21/9fa768] Submitted process > snp:merge_pileup_and_full_vars (8)
[ec/e50509] Submitted process > snp:merge_pileup_and_full_vars (17)
[46/7b0c8e] Submitted process > snp:merge_pileup_and_full_vars (9)
[6e/dc2c25] Submitted process > snp:merge_pileup_and_full_vars (19)
[e8/852cc5] Submitted process > snp:merge_pileup_and_full_vars (5)
[49/7fe045] Submitted process > snp:merge_pileup_and_full_vars (22)
[f5/9dc03a] Submitted process > snp:merge_pileup_and_full_vars (23)
[ef/0bb2c9] Submitted process > snp:merge_pileup_and_full_vars (21)
[10/5b0b35] Submitted process > snp:merge_pileup_and_full_vars (24)
[b1/3d90ea] Submitted process > snp:merge_pileup_and_full_vars (20)
[62/afcde4] Submitted process > snp:post_clair_phase_contig (1)
[06/677dbd] Submitted process > snp:post_clair_phase_contig (2)
[9f/e665d6] Submitted process > snp:post_clair_phase_contig (3)
[66/754e6d] Submitted process > snp:post_clair_phase_contig (4)
[29/f91fa7] Submitted process > snp:post_clair_phase_contig (5)
[1c/2f58da] Submitted process > snp:post_clair_phase_contig (6)
[e1/1d2891] Submitted process > snp:post_clair_phase_contig (7)
[a4/a675f8] Submitted process > snp:post_clair_phase_contig (8)
[8f/36b45e] Submitted process > snp:post_clair_phase_contig (9)
[a1/e3f191] Submitted process > snp:post_clair_phase_contig (10)
[b1/573bfc] Submitted process > snp:post_clair_phase_contig (11)
[2e/d62098] Submitted process > snp:post_clair_phase_contig (12)
[88/ac4c9c] Submitted process > snp:post_clair_phase_contig (13)
[e9/6c3bb2] Submitted process > snp:post_clair_phase_contig (14)
[a4/a2e64e] Submitted process > snp:post_clair_phase_contig (15)
[07/d4d626] Submitted process > snp:post_clair_phase_contig (16)
[d2/90e361] Submitted process > snp:post_clair_phase_contig (17)
[7d/6cd55b] Submitted process > snp:post_clair_phase_contig (18)
[b5/f2c0c5] Submitted process > snp:post_clair_phase_contig (19)
[b6/739199] Submitted process > snp:post_clair_phase_contig (20)
[0e/947bb2] Submitted process > snp:post_clair_phase_contig (21)
[36/78193f] Submitted process > snp:post_clair_phase_contig (22)
[8b/30af76] Submitted process > snp:post_clair_phase_contig (23)
[43/a7f64e] Submitted process > snp:post_clair_phase_contig (24)
[12/d8c272] Submitted process > snp:post_clair_contig_haplotag (1)
[1f/1f4cb9] Submitted process > snp:post_clair_contig_haplotag (2)
[4a/59381a] Submitted process > snp:post_clair_contig_haplotag (3)
[6b/fb3e3e] Submitted process > snp:post_clair_contig_haplotag (4)
[95/47cf1c] Submitted process > snp:post_clair_contig_haplotag (5)
[ec/c97f20] Submitted process > snp:post_clair_contig_haplotag (6)
[e1/e61c22] Submitted process > snp:post_clair_contig_haplotag (7)
[f2/d6ecd5] Submitted process > snp:post_clair_contig_haplotag (8)
[e3/d3b17f] Submitted process > snp:post_clair_contig_haplotag (9)
[10/f1d33e] Submitted process > snp:post_clair_contig_haplotag (10)
[b3/6638ce] Submitted process > snp:post_clair_contig_haplotag (11)
[26/31eb5b] Submitted process > snp:post_clair_contig_haplotag (12)
[ff/242c7f] Submitted process > snp:post_clair_contig_haplotag (13)
[91/fdde73] Submitted process > snp:post_clair_contig_haplotag (14)
[2f/b388bd] Submitted process > snp:post_clair_contig_haplotag (15)
[26/1fe48e] Submitted process > snp:post_clair_contig_haplotag (16)
[5d/294c73] Submitted process > snp:post_clair_contig_haplotag (17)
[a4/20cea2] Submitted process > snp:post_clair_contig_haplotag (18)
[1e/3178fb] Submitted process > snp:post_clair_contig_haplotag (19)
[9c/2ba520] Submitted process > snp:post_clair_contig_haplotag (20)
[0e/a9b41a] Submitted process > snp:post_clair_contig_haplotag (21)
[22/05e5dd] Submitted process > snp:post_clair_contig_haplotag (22)
[70/502049] Submitted process > snp:post_clair_contig_haplotag (23)
[3c/0ddc74] Submitted process > snp:aggregate_all_variants (1)
[91/fc7618] Submitted process > snp:post_clair_contig_haplotag (24)
[e0/d128b1] Submitted process > snp:haploblocks_snp (1)
[58/de4181] Submitted process > mod:modkit_phase (1)
[f5/3f0f3f] Submitted process > mod:modkit_phase (2)
[b7/bdba5e] Submitted process > cnv_spectre:callCNV (1)
ERROR ~ Error executing process > 'cnv_spectre:callCNV (1)'
Caused by:
  Process `cnv_spectre:callCNV (1)` terminated with an error exit status (1)
Command executed:
  spectre CNVCaller         --bin-size 1000         --threshhold-quantile 10         --dist-proportion 0.3         --coverage readstats/         --sample-id 23C8111791_DMPK         --output-dir spectre_output/         --reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fna         --blacklist grch38_blacklist_0.3         --min-cnv-len 80000         --snv 23C8111791_DMPK.wf_snp.vcf.gz         --metadata grch38_metadata
Command exit status:
  1
Command output:
  (empty)
Command error:
  spectre::INFO> Spectre version: 0.2.2
  spectre::INFO> Spectre enabled
  spectre::INFO> Extraction of metadata is activated
  spectre::INFO> Extracting metadata from resource: data/grch38_metadata.mdr
  spectre::INFO> Using blacklist from resource: data/grch38_blacklist_0.3.bed
  spectre::INFO> Spectre calculating for: readstats and bin size: 1000
  spectre::INFO> Data normalization and outlier removal (right tail)
  spectre::INFO> Parsing VCF to AF freqs file
  spectre::INFO> Thresholds for coverage, lower (Q10.0): None, upper(Q90.0): None
  multiprocessing.pool.RemoteTraceback: 
  """
  Traceback (most recent call last):
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 125, in worker
      result = (True, func(*args, **kwds))
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
      return list(map(*args))
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/main.py", line 120, in outside_spectre_worker
      worker.cnv_call()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/spectreCNV.py", line 101, in cnv_call
      self.cnv_analysis.data_normalization()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/analysis/analysis.py", line 172, in data_normalization
      self.lower_2n_threshold = coverage_lower_threshold / genome_median * self.ploidy
  TypeError: unsupported operand type(s) for /: 'NoneType' and 'NoneType'
  """

  The above exception was the direct cause of the following exception:

  Traceback (most recent call last):
    File "/opt/custflow/epi2meuser/conda/bin/spectre", line 10, in <module>
      sys.exit(run_main())
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/main.py", line 506, in run_main
      spectre_run.spectre_exe()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/main.py", line 274, in spectre_exe
      results = pool.map(outside_spectre_worker, tuple(spectre_instructions))
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 364, in map
      return self._map_async(func, iterable, mapstar, chunksize).get()
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 771, in get
      raise self._value
  TypeError: unsupported operand type(s) for /: 'NoneType' and 'NoneType'
Work dir:
  /mnt/d/epi2melabs/instances/wf-human-variation_01J2JDMS09VVSZDYG8QTMXKH51/work/b7/bdba5e9da33db589928a2f3010ad28
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
 -- Check '/mnt/d/epi2melabs/instances/wf-human-variation_01J2JDMS09VVSZDYG8QTMXKH51/nextflow.log' file for details
WARN: Killing running tasks (4)

Application activity log entry

There is no red item. Everything is in green Completed state.

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

yes

Other demo data information

No response

[vlshesketh]

Hi @nikelau thanks for your interest in the workflow. Can I please check, are you running the workflow on adaptive sampling data? If so then we would recommend trying QDNAseq instead of Spectre, as the latter isn't suitable for use with adaptive sampling.

[nikelau]

oh thanks Sirisha! yes i am using adaptive sampling. let me try again. by the way i tried the same set of data on two different windows machines (slightly different specs), while the other one (after deleting the TR BED as in another issue on github) worked using QDNAseq. it can sometimes be inconsistent even in terms of which bug will occur. adaptive sampling is great for low cost human applications, and it would be great if there could be specific workflows that provides best tools and settings for e.g. exomes or panels in addition to human genome. please consider! thanks!

[vlshesketh]

Hi, thank you for your comment re: adaptive sampling and exams/panels. We are in the process of revising our documentation around the options/settings which can be used for both Spectre and QDNAseq so please keep an eye on the repo for updates.

I'll close this issue for now but please feel free to re-open or create a new issue if you have any further problems with CNV calling.