❌ genomeassembler/test_full failed 😿 Run Name jovial_ptolemy Duration 6h 28m 38s Status ❌ Failed Error Message

(more omitted..)
LINKS_CPP -f assembly.fa -s readfile.fof   -d 500,2000,5000 -k 15 -t 40,200 -j 4 -l 5 -o 0 -e 0.1 -z 500 -p 0.001 -b test_hifi_hifiasm_links -v 0 -x 0
LINKS running options:
  -f assembly.fa
  -s readfile.fof
  -d 500,2000,5000
  -k 15
  -j 4
  -t 40,200
  -o 0
  -e 0.1
  -l 5
  -a 0.3
  -z 500
  -b test_hifi_hifiasm_links
  -r 
  -p 0.001
  -x 0
  -v 0
STAGE: Bloom filter construction/read
- Number of BF Elements: 180203732
- Input file path: test_hifi_hifiasm_links
- Input file: assembly.fa
- kmersize: 15
- m: 2590894920
- fpr: 0.001
- hashFct: 9
- Filter output file : 15
Writing Bloom filter to disk (test_hifi_hifiasm_links.bloom)
Bloom filter generated or loaded in: 0h 1m 6s 252ms
STAGE: Reading sequence reads
Reading: singles_hifi.fastplong.fastq
Processed read count: 100000 - 200000 - 300000 - 40000012:58PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
 - 500000 - 600000 - 696921
Read fasta stage completed in: 0h 5m 58s 295ms
STAGE: Reading contigs
Reading: assembly.fa
Processed read count: 760
1:03PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
[2026-09-10 13:03:14.845] [WARN] Warn  (dumprestore.c:235): predump failed, starting new chain for future dumps
[2026-09-10 13:03:14.846] [ERROR] Error (exec.c:102): incremental dump failed with code: -52
make: *** [/usr/local/bin/LINKS-make-real:122: test_hifi_hifiasm_links.tigpair_checkpoint.tsv] Killed
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.5TB, min:2.4TB, max:3.5TB, end:3.5TB
    clone_namespace: false
    download: 47210.36MB, drops:0, skip:0, sync:0, req:370
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 169466.41MB, drops:0, skip:0, sync:79, req:1402

Command Line

nextflow run '<https://github.com/nf-core/genomeassembler>' -name jovial_ptolemy -params-file '<https://api.cloud.seqera.io/ephemeral/_EAK6cYTaoH1sc7FRrbaOg.json>' -with-tower -r dev -profile test_full

Sep 10, 2026 at 1:05 PM