❌ genomeassembler/test_full failed 😿 Run Name jovial_ritchie Duration 6h 17m 13s Status ❌ Failed Error Message

(more omitted..)
8:24PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
Running Command: LINKS-make LINKS draft=assembly.fa readsFof=readfile.fof d=500,2000,5000  t=40,200 j=4      b=test_hifiasm_hifiasm_links     
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_hifiasm_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_hifiasm_hifiasm_links
  -r 
  -p 0.001
  -x 0
  -v 0
STAGE: Bloom filter construction/read
- Number of BF Elements: 178404349
- Input file path: test_hifiasm_hifiasm_links
- Input file: assembly.fa
- kmersize: 15
- m: 2565024136
- fpr: 0.001
- hashFct: 9
- Filter output file : 15
Writing Bloom filter to disk (test_hifiasm_hifiasm_links.bloom)
Bloom filter generated or loaded in: 0h 1m 2s 573ms
STAGE: Reading sequence reads
Reading: test_hifiasm_hifiasm_ont.fastplong.fastq
Processed read count: 100000 - 200000 - 300000 - 400000 - 500000 - 600000 - 700000 - 800000 - 900000 - 1000000 - 1100000 - 1200000 - 1300000 - 1400000 - 1500000 - 1600000 - 1700000 - 1800000 - 1900000 - 2000000 - 2100000 - 2200000 - 2300000 - 2400000 - 2500000 - 26000008:29PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
 - 2700000 - 2800000 - 2900000 - 3000000 - 3100000 - 3200000 - 3300000 - 3400000 - 3500000 - 3600000 - 3700000 - 3800000 - 3900000 - 4000000 - 4089945
Read fasta stage completed in: 0h 5m 30s 204ms
STAGE: Reading contigs
Reading: assembly.fa
Processed read count: 759
8:34PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
make: *** [/usr/local/bin/LINKS-make-real:122: test_hifiasm_hifiasm_links.tigpair_checkpoint.tsv] Killed
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.8TB, min:2.7TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 13657.73MB, drops:0, skip:0, sync:0, req:108
    fu...

Command Line

nextflow run '<https://github.com/nf-core/genomeassembler>' -name jovial_ritchie -params-file '<https://api.cloud.seqera.io/ephemeral/_lpQRt0837-icM-tOUcULA.json>' -with-tower -r dev -profile test_full

Sep 10, 2026 at 8:35 PM