Hi, I recently ran nextdenovo and while the run was “successful” and produced assembly stats and a configuration file, the fasta files were empty. There seems to be an error writing the file: here is the error log:
[2207 INFO] 2023-11-20 08:15:53 seed_cns finished, and final corrected reads file:
[2207 INFO] 2023-11-20 08:15:53 e[35m /data/jwd02f/main/064/835/64835575/working/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta e[0m
[2207 INFO] 2023-11-20 08:15:53 Total jobs: 36
[2207 INFO] 2023-11-20 08:15:53 Submitted jobID:[1035536] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align01/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:53 Submitted jobID:[1035605] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align02/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:54 Submitted jobID:[1035716] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align03/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:54 Submitted jobID:[1035804] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align04/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:55 Submitted jobID:[1035895] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align05/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:55 Submitted jobID:[1035964] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align06/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:56 Submitted jobID:[1036032] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align07/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 08:15:56 Submitted jobID:[1036105] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align08/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 17:09:31 Submitted jobID:[4105445] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align09/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 21:42:47 Submitted jobID:[1865934] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align10/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 22:31:08 Submitted jobID:[2148163] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align11/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 22:53:43 Submitted jobID:[2221028] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align12/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 23:05:58 Submitted jobID:[2247414] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align13/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 23:14:49 Submitted jobID:[2273915] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align14/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-20 23:22:07 Submitted jobID:[2308518] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align15/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 00:27:28 Submitted jobID:[2468162] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align16/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 01:19:44 Submitted jobID:[2659054] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align17/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 09:27:17 Submitted jobID:[2241251] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align18/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 09:32:46 Submitted jobID:[2292822] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align19/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 11:15:07 Submitted jobID:[661995] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align20/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 12:16:39 Submitted jobID:[883421] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align21/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 13:06:26 Submitted jobID:[1049957] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align22/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 13:21:22 Submitted jobID:[1089742] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align23/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 13:34:17 Submitted jobID:[1115358] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align24/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 15:19:13 Submitted jobID:[1485608] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align25/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 21:55:37 Submitted jobID:[3256643] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align26/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 22:35:04 Submitted jobID:[3415631] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align27/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-21 23:48:04 Submitted jobID:[3669045] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align28/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 00:19:23 Submitted jobID:[3764611] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align29/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 03:26:35 Submitted jobID:[236313] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align30/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 03:35:02 Submitted jobID:[279237] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align31/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 03:36:29 Submitted jobID:[286250] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align32/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 04:25:40 Submitted jobID:[461650] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align33/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 08:36:25 Submitted jobID:[1469763] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align34/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 12:23:46 Submitted jobID:[2408917] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align35/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 12:53:23 Submitted jobID:[2477481] jobCmd:[/data/jwd02f/main/064/835/64835575/working/02.cns_align/02.cns_align.sh.work/cns_align36/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:50:36 cns_align done
[2207 INFO] 2023-11-22 18:50:41 Total jobs: 1
[2207 INFO] 2023-11-22 18:50:41 Submitted jobID:[4091699] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:36 ctg_graph done
[2207 INFO] 2023-11-22 18:52:38 Total jobs: 8
[2207 INFO] 2023-11-22 18:52:38 Submitted jobID:[4100511] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align1/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:39 Submitted jobID:[4100538] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align2/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:39 Submitted jobID:[4100584] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:40 Submitted jobID:[4100626] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align4/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:40 Submitted jobID:[4100669] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align5/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:41 Submitted jobID:[4100713] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align6/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:41 Submitted jobID:[4100760] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align7/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 18:52:42 Submitted jobID:[4100810] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align8/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:43 ctg_align done
[2207 INFO] 2023-11-22 19:36:43 Total jobs: 8
[2207 INFO] 2023-11-22 19:36:43 Submitted jobID:[4187932] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns1/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:44 Submitted jobID:[4187985] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns2/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:44 Submitted jobID:[4188052] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns3/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:45 Submitted jobID:[4188089] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns4/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:45 Submitted jobID:[4188143] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns5/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:46 Submitted jobID:[4188210] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns6/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:46 Submitted jobID:[4188256] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns7/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:36:47 Submitted jobID:[4188301] jobCmd:[/data/jwd02f/main/064/835/64835575/working/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns8/nextDenovo.sh] in the local_cycle.
[2207 INFO] 2023-11-22 19:37:20 ctg_cns done
[2207 INFO] 2023-11-22 19:37:20 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align1/input.seed.008.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:20 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align2/input.seed.004.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:20 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/input.seed.001.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:20 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align4/input.seed.005.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:20 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align5/input.seed.003.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:21 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align6/input.seed.007.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:21 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align7/input.seed.002.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:21 remove temporary result: /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/02.ctg_align.sh.work/ctg_align8/input.seed.006.2bit.sort.bam
[2207 INFO] 2023-11-22 19:37:21 nextDenovo finished
[2207 INFO] 2023-11-22 19:37:21 final assembly file:
[2207 INFO] 2023-11-22 19:37:21 e[35m /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/nd.asm.fasta e[0m
[2207 INFO] 2023-11-22 19:37:21 final stat file:
[2207 INFO] 2023-11-22 19:37:21 e[35m /data/jwd02f/main/064/835/64835575/working/03.ctg_graph/nd.asm.fasta.stat e[0m
[2207 INFO] 2023-11-22 19:37:21 asm stat:
[2207 INFO] 2023-11-22 19:37:21
Type Length (bp) Count (#)
N10 127538 10
N20 95373 27
N30 76350 49
N40 69168 74
N50 61733 102
N60 56036 133
N70 50955 167
N80 45846 205
N90 41769 246
Min. 27408 -
Max. 304228 -
Ave. 61478 -
Total 18259195 297