nrhorner
commented
7 months ago Hi @BethHudson-Lund Can you share your log file please?
Thanks,
Neil
Closed BethHudson-Lund closed 2 months ago
nrhorner
commented
7 months ago Hi @BethHudson-Lund Can you share your log file please?
Thanks,
Neil
BethHudson-Lund
commented
7 months ago Thanks for your reply! Do you need all the information from .nextflow.log? It is huge!
I have just seen a similar issue reported with minimap2 but this is happening for me with other steps in the pipeline too eg. preprocess reads and fastcat. Is the trace.txt enough as I saw this reported in the other issue comment? I have encountered a few errors (including one with JAFFAL in this run) so many steps are cached from previous runs, but have been able to fix apart from the running a single step.
Let me know if you need any more information and I am happy to find. Thanks so much!
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
5 85/ce4e85 3024845 pipeline:getParams CACHED 0 2024-01-26 11:30:53.043 1.2s 23ms 22.8% 0 0 82.4 KB 2.3 KB
2 cf/3d22f7 3852108 pipeline:decompress_annotation CACHED 0 2024-01-29 17:29:16.922 7.9s 6s 94.6% 2.5 MB 7.1 MB 47.6 MB 1.5 GB
4 05/8b55ab 3857641 pipeline:build_minimap_index (1) CACHED 0 2024-01-29 17:31:03.618 1m 19s 1m 15s 149.0% 11.3 GB 14 GB 2.9 GB 6.1 GB
1 24/a6773c 3852114 validate_sample_sheet CACHED 0 2024-01-29 17:29:16.944 7.8s 5.7s 51.8% 100.6 MB 327 MB 18.6 MB 602 B
3 81/56ca84 3852934 pipeline:getVersions CACHED 0 2024-01-29 17:29:24.785 11.3s 10.2s 44.3% 79.9 MB 278.5 MB 39.4 MB 3 KB
11 7d/d96ea8 3927600 fastcat (5) CACHED 0 2024-01-29 19:25:09.495 4m 21s 4m 20s 342.9% 15.4 MB 372.4 MB 21.6 GB 21.8 GB
8 90/484967 3859277 fastcat (2) CACHED 0 2024-01-29 17:32:23.065 12m 15s 12m 14s 174.1% 15.5 MB 373.5 MB 44.2 GB 44.9 GB
13 3e/7a7015 3885520 fastcat (7) CACHED 0 2024-01-29 17:53:03.614 1m 10s 1m 9s 325.5% 15.3 MB 372.5 MB 5.5 GB 5.6 GB
6 bc/e02d6c 3854357 pipeline:preprocess_ref_annotation CACHED 0 2024-01-29 17:29:36.073 4.6s 3.1s 89.6% 3.4 MB 6.4 MB 1.5 GB 1.5 GB
7 5c/3de038 3852945 fastcat (1) CACHED 0 2024-01-29 17:29:24.880 1m 39s 1m 38s 162.9% 15 MB 371.9 MB 5.3 GB 5.4 GB
14 77/9d3373 3935407 fastcat (8) CACHED 0 2024-01-29 19:29:30.903 4m 12s 4m 10s 346.3% 15.2 MB 372.2 MB 21.3 GB 21.4 GB
10 e4/97c519 3880881 fastcat (4) CACHED 0 2024-01-29 17:50:24.239 2m 1m 59s 345.9% 36.2 MB 1.4 GB 9.9 GB 9.9 GB
16 12/cc92d5 3981303 fastcat (10) CACHED 0 2024-01-29 20:09:22.540 52.9s 52.3s 342.7% 36 MB 1.4 GB 4.5 GB 4.5 GB
9 dd/8e2351 3942322 fastcat (3) CACHED 0 2024-01-29 19:33:42.875 26m 2s 26m 1s 336.3% 37.2 MB 1.4 GB 129.8 GB 130.7 GB
21 fc/fcdbd5 3887572 fastcat (12) CACHED 0 2024-01-29 17:54:13.435 2m 18s 2m 18s 326.4% 15 MB 371.9 MB 11 GB 11.1 GB
12 96/7ff04e 3966439 fastcat (6) CACHED 0 2024-01-29 20:00:35.850 2m 46s 2m 46s 339.1% 35.8 MB 1.4 GB 13.7 GB 13.9 GB
22 3f/7391dc 3971810 fastcat (13) CACHED 0 2024-01-29 20:03:22.253 3m 36s 3m 36s 337.5% 35.2 MB 1.4 GB 18.3 GB 18.6 GB
23 32/62bdbd 3978047 fastcat (14) CACHED 0 2024-01-29 20:06:58.620 2m 24s 2m 23s 341.8% 14.7 MB 372.7 MB 12.3 GB 12.4 GB
15 c3/3ced05 3964707 fastcat (9) CACHED 0 2024-01-29 19:59:44.550 51.3s 50.6s 336.7% 14.9 MB 371.9 MB 4.1 GB 4.1 GB
17 4f/c90826 3883952 fastcat (11) CACHED 0 2024-01-29 17:52:24.127 39.5s 38.9s 324.0% 14.9 MB 371.9 MB 3 GB 3 GB
24 af/39ae34 3983165 fastcat (15) CACHED 0 2024-01-29 20:10:15.471 4m 29s 4m 28s 335.7% 36.6 MB 1.4 GB 22 GB 22.2 GB
25 b0/2aa9b9 4051440 pipeline:preprocess_reads (2) CACHED 0 2024-01-29 20:44:03.434 1h 28m 7s 1h 28m 7s 210.5% 1.4 GB 7.4 GB 77 GB 45.3 GB
20 58/728c02 3927933 pipeline:collectFastqIngressResultsInDir (2) CACHED 0 2024-01-29 19:25:11.208 554ms 59ms 11.0% 2.9 MB 7.6 MB 98.2 KB 325 B
18 a9/4a4c59 433902 pipeline:collectFastqIngressResultsInDir (6) CACHED 0 2024-01-30 10:16:22.282 763ms 40ms 41.9% 0 0 98.2 KB 326 B
29 26/b527ad 27453 pipeline:preprocess_reads (4) CACHED 0 2024-01-29 22:46:47.242 13m 2s 13m 1s 236.5% 1.3 GB 7.2 GB 12 GB 7.2 GB
27 18/684ca4 3928181 pipeline:collectFastqIngressResultsInDir (1) CACHED 0 2024-01-29 19:25:11.776 529ms 25ms 20.6% 0 0 98.2 KB 325 B
26 f8/ffb2b0 3927607 pipeline:collectFastqIngressResultsInDir (4) CACHED 0 2024-01-29 19:25:09.505 1.7s 19ms 24.0% 0 0 98.2 KB 325 B
28 4b/dce4fc 433895 pipeline:collectFastqIngressResultsInDir (3) CACHED 0 2024-01-30 10:16:22.265 773ms 29ms 16.8% 0 0 98.2 KB 326 B
32 ef/00ba70 3928343 pipeline:collectFastqIngressResultsInDir (3) CACHED 0 2024-01-29 19:25:12.319 451ms 28ms 19.5% 0 0 98.2 KB 325 B
19 5d/8a53f2 479661 pipeline:preprocess_reads (6) CACHED 0 2024-01-30 10:25:24.194 51m 22s 51m 21s 230.2% 1.4 GB 7.2 GB 41.1 GB 23.8 GB
31 90/ce060d 3990692 fastcat (16) CACHED 0 2024-01-29 20:14:44.017 2m 1s 2m 340.8% 14.8 MB 372.1 MB 9.5 GB 9.6 GB
44 ca/fbd236 3995739 fastcat (21) CACHED 0 2024-01-29 20:16:50.610 1m 25s 1m 24s 333.5% 16.6 MB 1.4 GB 7.1 GB 7.1 GB
40 72/fb1262 564031 pipeline:preprocess_reads (11) CACHED 0 2024-01-30 11:44:29.751 10m 5s 10m 5s 226.8% 1.4 GB 7.1 GB 10.6 GB 6 GB
30 c9/b819c8 4123698 pipeline:preprocess_reads (1) CACHED 0 2024-01-29 22:12:10.721 12m 34s 12m 33s 230.6% 1.3 GB 7.2 GB 11.5 GB 7.1 GB
45 58/cede9e 4040167 fastcat (22) CACHED 0 2024-01-29 20:40:21.235 1m 2s 1m 1s 296.3% 14.3 MB 371.6 MB 5.4 GB 5.5 GB
35 2e/7df0ef 4028793 fastcat (18) CACHED 0 2024-01-29 20:36:56.572 3m 25s 3m 24s 308.2% 14.9 MB 371.9 MB 18 GB 18.3 GB
33 a7/5b20c9 4150085 fastcat (17) CACHED 0 2024-01-29 22:25:06.761 3m 2s 3m 1s 305.2% 42.8 MB 1.4 GB 16.9 GB 17.1 GB
34 d2/38ccd8 434539 pipeline:collectFastqIngressResultsInDir (11) CACHED 0 2024-01-30 10:16:23.064 510ms 25ms 31.0% 0 0 98.2 KB 326 B
37 d3/8a5ddf 3998255 pipeline:preprocess_reads (3) CACHED 0 2024-01-29 20:18:15.687 18m 25s 18m 24s 207.3% 1.5 GB 7.3 GB 20.2 GB 11.4 GB
36 49/6f65be 393869 pipeline:preprocess_reads (3) CACHED 0 2024-01-30 09:36:03.857 40m 18s 40m 17s 204.1% 1.5 GB 7.4 GB 39.4 GB 21.7 GB
42 73/97c7f5 611401 pipeline:preprocess_reads (8) CACHED 0 2024-01-30 12:05:18.018 5h 17m 35s 5h 17m 33s 235.8% 1.6 GB 7.6 GB 239 GB 138.8 GB
39 86/b89efc 4025518 fastcat (20) CACHED 0 2024-01-29 20:36:40.205 16.4s 15s 236.2% 14.3 MB 372.6 MB 940.7 MB 943.5 MB
38 7d/711e6f 3995066 fastcat (19) CACHED 0 2024-01-29 20:16:45.164 5.4s 5s 322.1% 14.5 MB 371.7 MB 409.2 MB 411.7 MB
47 d9/3af4b1 4045449 fastcat (23) CACHED 0 2024-01-29 20:41:23.107 2m 40s 2m 40s 334.2% 35.7 MB 1.4 GB 13.6 GB 13.8 GB
41 e1/5c830b 434529 pipeline:collectFastqIngressResultsInDir (8) CACHED 0 2024-01-30 10:16:23.051 386ms 50ms 14.3% 0 0 98.2 KB 326 B
52 fb/50985d 434553 pipeline:collectFastqIngressResultsInDir (9) CACHED 0 2024-01-30 10:16:23.072 510ms 35ms 27.0% 0 0 98.2 KB 326 B
43 f3/32c12e 433916 pipeline:collectFastqIngressResultsInDir (7) CACHED 0 2024-01-30 10:16:22.296 760ms 30ms 34.9% 0 0 98.2 KB 326 B
53 48/91a26f 3928590 pipeline:collectFastqIngressResultsInDir (5) CACHED 0 2024-01-29 19:25:12.776 427ms 19ms 50.7% 0 0 98.2 KB 325 B
56 8b/302f81 4146324 fastcat (24) CACHED 0 2024-01-29 22:24:44.394 22.4s 20.6s 289.4% 14.8 MB 371.9 MB 1.5 GB 1.5 GB
60 a8/8c689d 435130 pipeline:collectFastqIngressResultsInDir (15) CACHED 0 2024-01-30 10:16:23.481 363ms 29ms 39.6% 0 0 98.2 KB 326 B
64 fb/7ddcfe 130076 fastcat (28) CACHED 0 2024-01-29 23:36:57.479 1m 14s 1m 14s 341.6% 14.8 MB 371.9 MB 7 GB 7.1 GB
58 4d/b904be 19989 fastcat (25) CACHED 0 2024-01-29 22:43:46.142 3m 1s 3m 327.0% 35.3 MB 1.4 GB 14.4 GB 14.6 GB
62 3a/c08599 452986 fastcat (26) CACHED 0 2024-01-30 10:18:57.607 2m 18s 2m 17s 289.0% 15.1 MB 372.8 MB 11 GB 11.1 GB
63 2b/aaae9c 4190906 fastcat (27) CACHED 0 2024-01-29 22:36:26.268 4m 33s 4m 32s 310.2% 14.8 MB 371.9 MB 24.5 GB 24.7 GB
61 41/7948c6 433910 pipeline:collectFastqIngressResultsInDir (10) CACHED 0 2024-01-30 10:16:22.289 761ms 51ms 25.2% 2.7 MB 3.8 MB 98.2 KB 326 B
48 99/489ef6 884327 pipeline:preprocess_reads (9) CACHED 0 2024-01-30 17:22:52.968 42m 44s 42m 44s 223.4% 1.4 GB 7.1 GB 34.4 GB 20.7 GB
54 79/3fb263 50205 pipeline:preprocess_reads (5) CACHED 0 2024-01-29 22:59:49.498 22m 4s 22m 4s 210.4% 1.3 GB 7.2 GB 21.5 GB 12.6 GB
65 1c/b81452 10593 fastcat (29) CACHED 0 2024-01-29 22:40:59.151 2m 47s 2m 46s 317.5% 15.2 MB 372.8 MB 14.7 GB 14.8 GB
57 53/1791af 1273355 pipeline:gene_fusions:jaffal (8) CACHED 0 2024-01-30 23:24:44.160 9m 31s 9m 31s 313.0% 19.5 GB 33.3 GB 9.9 GB 3.5 GB
80 2d/d6f9cf 587914 pipeline:preprocess_reads (10) CACHED 0 2024-01-30 11:54:35.067 10m 43s 10m 42s 235.2% 1.4 GB 7.1 GB 9.8 GB 5.6 GB
66 e6/a31d96 4181769 fastcat (30) CACHED 0 2024-01-29 22:33:38.961 2m 47s 2m 46s 313.5% 36.1 MB 1.4 GB 13.9 GB 14.1 GB
67 cc/aa67a8 1069091 pipeline:preprocess_reads (15) CACHED 0 2024-01-30 20:13:55.711 24m 33s 24m 32s 206.6% 1.3 GB 7.2 GB 23.6 GB 13.9 GB
50 12/056942 926169 pipeline:reference_assembly:map_reads (4) CACHED 0 2024-01-30 18:05:37.113 13m 49s 13m 48s 380.5% 10.9 GB 18.2 GB 10.3 GB 952.7 MB
51 81/a692c1 4146540 pipeline:gene_fusions:jaffal (2) CACHED 0 2024-01-29 22:24:45.020 15m 52s 15m 51s 329.9% 19.5 GB 33.3 GB 14.1 GB 5.3 GB
78 7a/8d5390 4161695 fastcat (31) CACHED 0 2024-01-29 22:28:08.588 3m 9s 3m 8s 296.7% 14.9 MB 372.8 MB 17.5 GB 17.7 GB
49 66/c701cd 97148 pipeline:gene_fusions:jaffal (4) CACHED 0 2024-01-29 23:29:49.379 3m 29s 3m 28s 258.8% 19.5 GB 33.3 GB 4.6 GB 596.3 MB
81 e6/fb49f3 3928817 pipeline:collectFastqIngressResultsInDir (6) CACHED 0 2024-01-29 19:25:13.212 567ms 19ms 50.8% 0 0 98.2 KB 325 B
87 c9/feb9c0 111717 fastcat (35) CACHED 0 2024-01-29 23:32:55.358 2m 19s 2m 19s 325.3% 39.7 MB 1.4 GB 13.9 GB 14 GB
75 af/ae15a1 2501190 pipeline:reference_assembly:map_reads (4) CACHED 0 2024-01-31 11:22:11.652 50m 10s 50m 9s 396.9% 13.1 GB 19.5 GB 13.9 GB 3.6 GB
55 a3/9abc8f 1193638 pipeline:reference_assembly:map_reads (2) CACHED 0 2024-01-30 21:41:57.258 1h 42m 46s 1h 42m 46s 401.9% 15.4 GB 20.2 GB 19.6 GB 7.6 GB
79 3f/e784d6 4174039 fastcat (32) CACHED 0 2024-01-29 22:31:17.627 2m 21s 2m 21s 315.3% 14.9 MB 371.9 MB 13.5 GB 13.6 GB
77 9c/c9b22f 1170344 pipeline:reference_assembly:map_reads (1) CACHED 0 2024-01-30 21:27:38.386 14m 19s 14m 18s 388.8% 11 GB 18 GB 10.2 GB 883.9 MB
76 55/1dd72c 1140441 pipeline:reference_assembly:map_reads (3) CACHED 0 2024-01-30 21:02:28.105 25m 10s 25m 10s 388.9% 11.2 GB 12.2 GB 11.2 GB 1.7 GB
73 55/5383d2 6336 pipeline:gene_fusions:jaffal (3) CACHED 0 2024-01-29 22:40:37.035 3m 28s 3m 27s 264.8% 19.5 GB 33.3 GB 4.7 GB 620.9 MB
71 0a/db1e3c 438008 pipeline:gene_fusions:jaffal (7) CACHED 0 2024-01-30 10:16:26.333 8m 24s 8m 24s 312.1% 19.5 GB 33.3 GB 7.8 GB 2.2 GB
85 32/821dba 434566 pipeline:collectFastqIngressResultsInDir (13) CACHED 0 2024-01-30 10:16:23.078 396ms 32ms 37.8% 0 0 98.2 KB 326 B
88 23/a66358 122065 fastcat (36) CACHED 0 2024-01-29 23:35:14.658 1m 43s 1m 42s 337.0% 14.9 MB 372 MB 9.3 GB 9.4 GB
72 4a/462bb0 4025760 pipeline:gene_fusions:jaffal (1) CACHED 0 2024-01-29 20:36:40.648 5m 17s 5m 17s 291.4% 19.5 GB 33.3 GB 5.5 GB 1005.6 MB
84 02/b51167 1018604 pipeline:preprocess_reads (13) CACHED 0 2024-01-30 19:19:55.510 54m 53m 59s 236.1% 1.4 GB 7.3 GB 42.3 GB 24.7 GB
92 03/ff1f4d 990519 pipeline:preprocess_reads (16) CACHED 0 2024-01-30 18:58:47.248 21m 8s 21m 8s 227.3% 1.3 GB 7.2 GB 19.7 GB 10.8 GB
94 f1/9f1002 2572640 pipeline:reference_assembly:map_reads (6) CACHED 0 2024-01-31 12:12:21.970 19m 31s 19m 30s 384.9% 11.3 GB 12.3 GB 11.4 GB 1.8 GB
90 1f/cd95d7 470456 fastcat (37) CACHED 0 2024-01-30 10:22:55.405 2m 29s 2m 28s 308.6% 36.1 MB 1.4 GB 12.9 GB 13 GB
93 4b/4e4601 435095 pipeline:collectFastqIngressResultsInDir (16) CACHED 0 2024-01-30 10:16:23.445 368ms 20ms 59.8% 0 0 98.2 KB 326 B
86 38/f67658 96805 fastcat (34) CACHED 0 2024-01-29 23:29:48.209 3m 7s 3m 5s 321.2% 15.1 MB 371.9 MB 17.6 GB 17.8 GB
82 23/aa164d 80263 pipeline:preprocess_reads (6) CACHED 0 2024-01-29 23:21:53.721 7m 54s 7m 54s 246.0% 1.4 GB 7.1 GB 7.7 GB 4.5 GB
96 40/457a69 468436 fastcat (38) CACHED 0 2024-01-30 10:22:31.790 23.6s 23.2s 273.7% 14.7 MB 372.5 MB 1.8 GB 1.8 GB
83 fe/349cc7 463211 fastcat (33) CACHED 0 2024-01-30 10:21:15.129 1m 17s 1m 16s 330.2% 14.8 MB 371.9 MB 6.8 GB 6.8 GB
102 ac/f091c6 435776 pipeline:collectFastqIngressResultsInDir (23) CACHED 0 2024-01-30 10:16:23.978 411ms 20ms 26.0% 0 0 98.2 KB 328 B
97 6a/a00d74 1112924 pipeline:preprocess_reads (20) CACHED 0 2024-01-30 20:44:12.279 18m 16s 18m 15s 246.6% 1.4 GB 7.1 GB 15.5 GB 8.8 GB
98 b4/76e8b5 114276 pipeline:gene_fusions:jaffal (5) CACHED 0 2024-01-29 23:33:18.015 4m 51s 4m 50s 269.1% 19.5 GB 33.3 GB 5.7 GB 1.2 GB
95 6d/b31dfa 435220 pipeline:collectFastqIngressResultsInDir (20) CACHED 0 2024-01-30 10:16:23.583 431ms 32ms 33.6% 0 0 98.2 KB 328 B
143 b0/94c6f0 436671 pipeline:collectFastqIngressResultsInDir (27) CACHED 0 2024-01-30 10:16:24.676 1.1s 17ms 25.0% 0 0 98.2 KB 328 B
123 ca/668469 950658 pipeline:preprocess_reads (14) CACHED 0 2024-01-30 18:19:25.972 39m 21s 39m 21s 224.6% 1.4 GB 7.2 GB 32.5 GB 19.2 GB
142 d9/5e5cee 436874 pipeline:collectFastqIngressResultsInDir (29) CACHED 0 2024-01-30 10:16:24.736 1.2s 21ms 69.9% 0 0 98.2 KB 328 B
136 3a/f2f066 435552 pipeline:collectFastqIngressResultsInDir (22) CACHED 0 2024-01-30 10:16:23.826 533ms 18ms 47.3% 0 0 98.2 KB 328 B
145 2e/31c02e 478582 pipeline:collectFastqIngressResultsInDir (35) CACHED 0 2024-01-30 10:24:50.811 498ms 19ms 53.4% 0 0 98.2 KB 328 B
114 e3/2163b6 1289280 fastcat (43) CACHED 0 2024-01-30 23:28:04.024 1m 55s 1m 55s 247.7% 15.3 MB 372 MB 9 GB 9 GB
124 63/c320e0 1100187 pipeline:preprocess_reads (18) CACHED 0 2024-01-30 20:38:28.703 3m 36s 3m 36s 258.1% 1.4 GB 7.1 GB 3.6 GB 2.1 GB
140 e2/ccfd43 435830 pipeline:collectFastqIngressResultsInDir (19) CACHED 0 2024-01-30 10:16:24.022 437ms 17ms 80.2% 0 0 98.2 KB 328 B
141 93/4bfc2a 436273 pipeline:collectFastqIngressResultsInDir (21) CACHED 0 2024-01-30 10:16:24.367 361ms 24ms 67.3% 0 0 98.2 KB 328 B
111 1d/91c3ea 1308951 fastcat (40) CACHED 0 2024-01-30 23:32:50.265 1m 13s 1m 12s 308.2% 14.9 MB 372 MB 6.3 GB 6.4 GB
113 e9/4d15c4 1286763 fastcat (42) CACHED 0 2024-01-30 23:27:31.111 32.9s 31.3s 212.8% 15 MB 373.2 MB 2 GB 2 GB
100 16/0f4386 1273025 fastcat (39) CACHED 0 2024-01-30 23:24:43.350 2m 48s 2m 47s 241.6% 15.3 MB 371.9 MB 12.5 GB 12.6 GB
125 1d/a47b83 1108584 pipeline:preprocess_reads (19) CACHED 0 2024-01-30 20:42:05.074 2m 7s 2m 7s 280.8% 1.3 GB 7.1 GB 3.1 GB 2 GB
139 45/ba1af0 435232 pipeline:collectFastqIngressResultsInDir (18) CACHED 0 2024-01-30 10:16:23.593 377ms 42ms 13.9% 0 0 98.2 KB 328 B
149 da/b2ebbd 437048 pipeline:collectFastqIngressResultsInDir (26) CACHED 0 2024-01-30 10:16:25.691 354ms 20ms 45.0% 0 0 98.2 KB 328 B
112 b5/69922f 1296644 fastcat (41) CACHED 0 2024-01-30 23:29:59.537 2m 51s 2m 50s 320.7% 15 MB 371.9 MB 14.8 GB 15 GB
137 c7/d6b9a0 435575 pipeline:collectFastqIngressResultsInDir (14) CACHED 0 2024-01-30 10:16:23.851 408ms 19ms 43.5% 0 0 98.2 KB 328 B
152 50/84dc53 437579 pipeline:collectFastqIngressResultsInDir (33) CACHED 0 2024-01-30 10:16:26.053 326ms 16ms 44.6% 0 0 98.2 KB 328 B
147 bf/8635a0 437145 pipeline:collectFastqIngressResultsInDir (30) CACHED 0 2024-01-30 10:16:25.773 363ms 15ms 26.6% 0 0 98.2 KB 328 B
144 7c/0eac2a 436307 pipeline:collectFastqIngressResultsInDir (24) CACHED 0 2024-01-30 10:16:24.395 1.2s 23ms 20.7% 0 0 98.2 KB 328 B
166 58/e52ad3 436927 pipeline:collectFastqIngressResultsInDir (28) CACHED 0 2024-01-30 10:16:25.638 348ms 21ms 42.7% 0 0 98.2 KB 328 B
171 19/850a57 436393 pipeline:collectFastqIngressResultsInDir (31) CACHED 0 2024-01-30 10:16:24.466 1.2s 883ms 1.1% 3.6 MB 7.4 MB 98.2 KB 327 B
153 f1/2884b7 437462 pipeline:collectFastqIngressResultsInDir (32) CACHED 0 2024-01-30 10:16:25.989 339ms 18ms 46.0% 0 0 98.2 KB 328 B
178 b0/5dd3a7 478730 pipeline:collectFastqIngressResultsInDir (36) CACHED 0 2024-01-30 10:24:51.316 402ms 20ms 49.2% 0 0 98.2 KB 328 B
167 d0/24e9d4 436168 pipeline:collectFastqIngressResultsInDir (25) CACHED 0 2024-01-30 10:16:24.266 391ms 18ms 50.1% 0 0 98.2 KB 328 B
133 d6/efdaa5 437713 pipeline:gene_fusions:jaffal (5) CACHED 0 2024-01-30 10:16:26.144 2m 31s 2m 31s 208.1% 19.5 GB 33.3 GB 4.1 GB 311.5 MB
170 1f/31744e 1273031 pipeline:collectFastqIngressResultsInDir (38) CACHED 0 2024-01-30 23:24:43.358 793ms 47ms 28.7% 1 MB 3.8 MB 98.2 KB 328 B
169 21/20cdf2 437474 pipeline:collectFastqIngressResultsInDir (34) CACHED 0 2024-01-30 10:16:25.998 355ms 38ms 16.8% 0 0 98.2 KB 328 B
183 08/e10531 2796442 pipeline:collectFastqIngressResultsInDir (34) CACHED 0 2024-01-31 17:24:14.086 321ms 28ms 20.8% 2.7 MB 3.8 MB 98.1 KB 326 B
182 c3/fb5f35 2795780 pipeline:collectFastqIngressResultsInDir (36) CACHED 0 2024-01-31 17:24:12.984 1.1s 21ms 10.4% 0 0 98.1 KB 326 B
46 06/fa057d 2809653 pipeline:preprocess_reads (9) COMPLETED 0 2024-01-31 17:34:11.356 25m 57s 25m 56s 195.8% 1.4 GB 7.3 GB 26.1 GB 15.2 GB
59 24/0195ed 2841634 pipeline:reference_assembly:map_reads (3) COMPLETED 0 2024-01-31 18:00:08.525 33m 11s 33m 11s 396.8% 13.4 GB 19.8 GB 15.7 GB 4.8 GB
70 ae/a297f6 2879326 pipeline:reference_assembly:map_reads (4) COMPLETED 0 2024-01-31 18:33:19.523 11m 57s 11m 56s 379.2% 10.6 GB 11.5 GB 10.1 GB 806.7 MB
91 12/54b25f 2901572 pipeline:reference_assembly:map_reads (9) COMPLETED 0 2024-01-31 18:45:16.407 30m 38s 30m 37s 400.5% 13.3 GB 19.6 GB 13.8 GB 3.5 GB
74 b4/6adc8c 2939588 pipeline:reference_assembly:map_reads (5) COMPLETED 0 2024-01-31 19:15:54.103 8h 16m 53s 8h 16m 52s 402.4% 17.3 GB 21.1 GB 48.7 GB 29.3 GB
99 e6/51fa15 3323985 pipeline:reference_assembly:map_reads (11) COMPLETED 0 2024-02-01 03:32:46.649 11m 20s 11m 19s 393.6% 10.7 GB 11.6 GB 10.3 GB 1014.2 MB
101 fa/27373b 3344103 pipeline:preprocess_reads (18) COMPLETED 0 2024-02-01 03:44:06.471 13m 32s 13m 31s 237.0% 1.4 GB 7.1 GB 12.2 GB 6.9 GB
108 a8/00b0c3 3368188 pipeline:split_bam (4) COMPLETED 0 2024-02-01 03:57:38.487 4.9s 3.1s 283.6% 243.2 MB 907.4 MB 117.9 MB 60.5 MB
119 80/245697 3368472 fastcat (46) COMPLETED 0 2024-02-01 03:57:43.395 28.9s 26.3s 276.5% 14.4 MB 371.6 MB 1.9 GB 1.9 GB
128 81/cdbb1a 3372514 fastcat (47) COMPLETED 0 2024-02-01 03:58:12.279 28.8s 26.3s 282.8% 14.3 MB 371.8 MB 1.8 GB 1.8 GB
117 91/ae41b2 3374749 fastcat (45) COMPLETED 0 2024-02-01 03:58:41.124 28.1s 26.4s 303.2% 14.8 MB 372 MB 2.1 GB 2.1 GB
132 78/39ddc9 3377117 pipeline:gene_fusions:jaffal (14) COMPLETED 0 2024-02-01 03:59:09.210 6m 53s 6m 52s 138.4% 19.5 GB 33.3 GB 5.3 GB 1006.7 MB
89 d7/9b257e 3377122 pipeline:gene_fusions:jaffal (9) COMPLETED 0 2024-02-01 03:59:09.217 11m 52s 11m 50s 169.2% 19.5 GB 33.3 GB 8.1 GB 2.4 GB
131 ef/a3bc05 3433108 pipeline:gene_fusions:jaffal (13) COMPLETED 0 2024-02-01 04:06:02.269 9m 39s 9m 38s 163.1% 19.5 GB 33.4 GB 8.6 GB 3.1 GB
172 da/3790f6 3497475 pipeline:collectFastqIngressResultsInDir (37) COMPLETED 0 2024-02-01 04:15:41.176 610ms 37ms 16.5% 2.8 MB 3.8 MB 98.2 KB 326 B
104 4a/27e74f 3471210 pipeline:gene_fusions:jaffal (12) COMPLETED 0 2024-02-01 04:11:01.286 7m 16s 7m 15s 186.3% 19.5 GB 33.3 GB 5.9 GB 1.3 GB
68 2c/317dbc 3513689 pipeline:gene_fusions:jaffal (4) FAILED 0 2024-02-01 04:18:17.517 5.8s 4.2s 1.9% 271.3 MB 9.3 GB 278.3 KB 88.1 KB
69 94/41e582 3368504 pipeline:gene_fusions:jaffal (5) ABORTED - 2024-02-01 03:57:43.401 - - - - - - -
154 c8/3f0a9d 3377132 pipeline:gene_fusions:jaffal (17) ABORTED - 2024-02-01 03:59:09.223 - - - - - - -
138 5e/9a97e1 3497638 pipeline:gene_fusions:jaffal (16) ABORTED - 2024-02-01 04:15:41.820 - - - - - - -
179 2f/63ffce 3514530 pipeline:collectFastqIngressResultsInDir (39) ABORTED - 2024-02-01 04:18:23.352 - - - - - - -Hi @BethHudson-Lund Sorry for taking so long to reply.
Could you attach the .nextflow.log to a response please? And I'll get straight back to you.
Thanks
nrhorner
commented
4 months ago Hi @BethHudson-Lund is this still an issue for you? If so please attach your log file to a reply please
nrhorner
commented
2 months ago Closing due to lack of response
Ask away!
Hi! I am currently running this pipeline for 47 samples with the following command:
nextflow run epi2me-labs/wf-transcriptomes \ --fastq /long_read_RNA/samples/ \ --ref_genome /hg38_ref.fna \ --transcriptome-source reference-guided \ --ref_annotation /long_read_RNA/REF/gencode.v45.primary_assembly.annotation.gtf.gz \ --jaffal_refBase /long_read_RNA/REF/jaffal_data_dir/ --jaffal_genome hg38 --jaffal_annotation genCode22 \ --sample_sheet samplesheet.csv \ -profile singularity \ --out_dir /long_read_RNA/epi2me/ \ -with-tower -resume \ --threads 4
Each fastq is in a subdirectory dictated by a sample sheet laid out like this:
barcode,alias sample1,sample1 sample2,sample2
I'm not sure if I haven't included a key argument or if I have laid this out wrong, but when monitoring via the tower I can see that only one step for one file is running at a time eg. nothing is running in parallel. This is taking significantly longer - is there any way you could help? Thanks so much!