Command terminated by signal 9 #292
Comments
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@Zoeyoungxy, how many Gb of RAM do you have? |
$ free -h |
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Can you share the data? |
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Sure, I am willing to share. But the data is quite large, with an uncompressed fasta of 73Gb. Can I send the gzipped fasta file to your email? |
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Thank you! |
Sure! Thank you! |
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@Zoeyoungxy, did you avoid such a problem with newer versions of PGGB? |
Hi all,
I got the error message while using the command
pggb -i /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa -o /home/zoey/wd_20230412/chr5 -n 210 -t 128 -p 98 -s 5000 -V 'CHM13v2:#:1000'The log is:
Starting pggb on 04-13-2023_15:59:49
Command: /home/zoey/anaconda3/envs/pggb/bin/pggb -i /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa -o /home/zoey/wd_20230412/chr5 -n 210 -t 128 -p 98 -s 5000 -V CHM13v2:#:1000
PARAMETERS
general:
input-fasta: /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa
output-dir: /home/zoey/wd_20230412/chr5
temp-dir: /home/zoey/wd_20230412/chr5
resume: false
compress: false
threads: 128
poa_threads: 128
wfmash:
version: v0.10.2-0-g2aaba27
segment-length: 5000
block-length: 25000
map-pct-id: 98
n-mappings: 210
no-splits: false
sparse-map: false
mash-kmer: 19
mash-kmer-thres: 0.001
exclude-delim: false
no-merge-segments: false
seqwish:
version: v0.7.8-0-gf362f6f
min-match-len: 19
sparse-factor: 0
transclose-batch: 10000000
smoothxg:
version: v0.6.8-0-ga8a0e9e
skip-normalization: false
n-haps: 210
path-jump-max: 0
edge-jump-max: 0
poa-length-target: 700,900,1100
poa-params: 1,19,39,3,81,1
poa_padding: 0.001
run_abpoa: false
run_global_poa: false
pad-max-depth: 100
write-maf: false
consensus-spec: false
consensus-prefix: Consensus_
block-id-min: .9800
block-ratio-min: 0
odgi:
version: v0.8.2-0-g8715c55
viz: true
layout: true
stats: false
gfaffix:
version: v0.1.4
reduce-redundancy: true
vg:
version: v1.46.0
deconstruct: CHM13v2:#:1000
reporting:
version: v1.14
multiqc: false
Running pggb
[wfmash::map] Reference = [/home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa]
[wfmash::map] Query = [/home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa]
[wfmash::map] Kmer size = 19
[wfmash::map] Window size = 226
[wfmash::map] Segment length = 5000 (read split allowed)
[wfmash::map] Block length min = 25000
[wfmash::map] Chaining gap max = 100000
[wfmash::map] Percentage identity threshold = 98%
[wfmash::map] Skip self mappings
[wfmash::map] Mapping output file = /dev/stdout
[wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[wfmash::map] Execution threads = 128
[wfmash::skch::Sketch::build] minimizers picked from reference = 675103571
[wfmash::skch::Sketch::index] unique minimizers = 1498281
[wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 19) ... (2011447, 1)
[wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 599723 times during lookup.
[wfmash::map] time spent computing the reference index: 764.234 sec
[wfmash::skch::Map::mapQuery] mapped 0.00% @ 0.00e+00 bp/s elapsed: 00:00:00:00 remain: 00:00:00:00
...
[wfmash::skch::Map::mapQuery] mapped 6.52% @ 9.70e+05 bp/s elapsed: 00:00:54:33 remain: 00:13:02:09Command terminated by signal 9
wfmash -s 5000 -l 25000 -p 98 -n 209 -k 19 -H 0.001 -X -t 128 --tmp-base /home/zoey/wd_20230412/chr5 /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa --approx-map
15954.21s user 5672.44s system 532% cpu 4063.87s total 39730540Kb max memory
I would like to know the reason that
Command terminated by signal 9occuerred and there any solutions to solve the problem?Any suggestions will be highly appreciated.
Thank You,
Zoey
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