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
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 >&, uint64t): 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