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Assertion `queryLen <= querySize' failed #251

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shuai19910911 opened this issue Jun 23, 2024 · 1 comment
Open

Assertion `queryLen <= querySize' failed #251

shuai19910911 opened this issue Jun 23, 2024 · 1 comment

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@shuai19910911
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shuai19910911 commented Jun 23, 2024

when I run this:
singularity exec $pggb_path/pggb_latest.sif wfmash -t 20 $genome_path/ganganF73.genome.fa.gz --query-file-list=/home/user/huyang/shuai/data/pan_test/genome/genome.txt > aln.paf

I got the Error: Assertion `queryLen <= querySize' failed.

[mashmap] MashMap v3.1.1
[mashmap] Reference = [/home/user/huyang/shuai/data/pan_test/genome/ganganF73.genome.fa.gz]
[mashmap] Query = [/home/user/huyang/shuai/data/pan_test/genome/no2127.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/quintaA.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/shengli3.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/tapidor3.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/westar.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/zheyou73.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/zs11.genome.fa.gz]
[mashmap] Kmer size = 19
[mashmap] Sketch size = 298
[mashmap] Segment length = 5000 (read split allowed)
[mashmap] Block length min = 25000
[mashmap] Chaining gap max = 20000
[mashmap] Mappings per segment = 1
[mashmap] Percentage identity threshold = 90%
[mashmap] Do not skip self mappings
[mashmap] Hypergeometric filter w/ delta = 0 and confidence 0.999
[mashmap] Mapping output file = /home/user/huyang/shuai/data/pan_test/combine_genome/wfmash-M3nGJ8
[mashmap] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[mashmap] Execution threads = 20
[mashmap::skch::Sketch::build] minmer windows picked from reference = 119006462
[mashmap::skch::Sketch::index] unique minmers = 29741018
[mashmap::skch::Sketch::computeFreqHist] Frequency histogram of minmer interval points = (2, 18506199) ... (42440, 1)
[mashmap::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minmers occurring >= 7642 times during lookup.
[wfmash::map] time spent computing the reference index: 51.6444 sec
[mashmap::skch::Map::mapQuery] mapped 100.00% @ 9.28e+06 bp/s elapsed: 00:00:12:41 remain: 00:00:00:00
[mashmap::skch::Map::mapQuery] count of mapped reads = 13478, reads qualified for mapping = 26603, total input reads = 26603, total input bp = 7069029650
[wfmash::map] time spent mapping the query: 7.63e+02 sec
[wfmash::map] mapping results saved in: /home/user/huyang/shuai/data/pan_test/combine_genome/wfmash-M3nGJ8
[wfmash::align] Reference = [/home/user/huyang/shuai/data/pan_test/genome/ganganF73.genome.fa.gz]
[wfmash::align] Query = [/home/user/huyang/shuai/data/pan_test/genome/no2127.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/quintaA.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/shengli3.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/tapidor3.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/westar.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/zheyou73.genome.fa.gz, /home/user/huyang/shuai/data/pan_test/genome/zs11.genome.fa.gz]
[wfmash::align] Mapping file = /home/user/huyang/shuai/data/pan_test/combine_genome/wfmash-M3nGJ8
[wfmash::align] Alignment identity cutoff = 72.00%
[wfmash::align] Alignment output file = /dev/stdout
[wfmash::align] time spent loading the reference index: 0.43 sec
[wfmash::align::computeAlignments] aligned 13.77% @ 5.73e+05 bp/s elapsed: 00:00:24:50 remain: 00:02:35:35

_wfmash: /wfmash/src/align/include/computeAlignments.hpp:510: void align::Aligner::doAlignment(std::stringstream&, align::MappingBoundaryRow&, const string&, const std::shared_ptr<std::_cxx11::basic_string >&, uint64_t): Assertion `queryLen <= querySize' failed.

/var/spool/slurm/d/job5358641/slurm_script: line 21: 152979 Aborted singularity exec $pggb_path/pggb_latest.sif wfmash -t 20 $genome_path/ganganF73.genome.fa.gz --query-file-list=/home/user/huyang/shuai/data/pan_test/genome/genome.txt > aln.paf

How do I solve this error?
The genome data were downloaded in http://cbi.hzau.edu.cn/cgi-bin/rape/download_ext

The log:
slurm-5358641.txt

@skyclub3
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skyclub3 commented Aug 5, 2024

Any idea...?

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