Closed Estel-Kitsune closed 7 months ago
Exit code 140 usually means resources were not enough. Check slurm to see whether it was out of memory, or a time out. My guess is probably a time out.
Content of .command.err
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO: Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
-----------------------------------------------------------------------------
tax-id : 57642
fasta : hifiasm-raw-default.asm.bp.p_ctg.fasta.gz
size : 252.6 MiB
split-fa : True
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
BLAST-div : gastropods
gx-div : anml:molluscs
w/same-tax: True
bin-dir : /usr/local/bin
gx-db : gxdb_all/all.gxi
gx-ver : Jan 9 2024 20:12:29; git:+branch--
output : ./hifiasm-decontaminated-default-hap0.taxonomy.rpt
-----------------------------------------------------------------------------
Warning: The host does not have enough physical memory for the gx-database.
The execution is likely to be extremely slow due to disk thrashing, and suitable only for tiny genomes (e.g. bacteria).
Virtual memory paging does not provide adequate performance.
See https://github.com/ncbi/fcs/wiki/FCS-GX for details.
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
[...]
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
Collecting masking statistics...
Using GX_NUM_CORES=12
egrep: warning: egrep is obsolescent; using grep -E
[...]
egrep: warning: egrep is obsolescent; using grep -E
Collected masking stats: 0.878724 Gbp; 24.3732s; 36.0528 Mbp/s. Baseline: 1.96825
Using GX_NUM_CORES=12
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
[...]
Yes, time limit: slurmstepd: error: JOB 45039282 ON r189 CANCELLED AT 2024-02-15T10:13:28 DUE TO TIME LIMIT
Error
Run info N E X T F L O W ~ version 22.10.2 Launching
https://github.com/NBISweden/Earth-Biogenome-Project-pilot
[awesome_wescoff] DSL2 - revision: 45ea5ddb38 [main]