Command terminated by signal 6

[emilio-r]

Hello again,

Yesterday I used docker to pull, and try, the latest available build of pggb. While some samples do work, running this one particular sample of ten genomes results in an error which terminates the run.
Is this due to the parameters, the sample, or is it the version?

Starting pggb on Fri Aug 20 09:28:30 CEST 2021

Command: /usr/local/bin/pggb -i ./indata/completes/Ten_global_refs_cleaned.fa -s 500 -p 85 -n 9 -P 1,9,16,2,41,1 -t 10 -v -C 1000 -L -o ./outdata/completes/cleaned

PARAMETERS

general:
  input-fasta:        ./indata/completes/Ten_global_refs_cleaned.fa
  output-dir:         ./outdata/completes/cleaned
  resume:             false
  pigz-compress:      false
  threads:            10
alignment:
  mapping-tool:       wfmash
  no-splits:          false
  segment-length:     500
  block-length:       1500
  no-merge-segments:  false
  map-pct-id:         85
  n-mappings:         9
  mash-kmer:          16
  exclude-delim:      false
seqwish:
  min-match-len:      19
  transclose-batch:   10000000
smoothxg:
  n-haps:             9
  path-jump-max:      100
  edge-jump-max:      0
  poa-length-target:  13117,13219
  poa-params:         1,9,16,2,41,1
  write-maf:          false
  consensus-prefix:   Consensus_
  consensus-spec:     1000
  split-min-depth:    2000
  block-id-min:       0
  block-ratio-min:    0
  poa_threads:        10
  poa_padding:        0.001
odgi:
  normalize:          false
  viz:                true
  layout:             true
  stats:              false
vg:
  deconstruct:        false  
reporting:
  multiqc:            false

Running pggb

[wfmash::map] Reference = [./indata/completes/Ten_global_refs_cleaned.fa]
[wfmash::map] Query = [./indata/completes/Ten_global_refs_cleaned.fa]
[wfmash::map] Kmer size = 16
[wfmash::map] Window size = 1
[wfmash::map] Segment length = 500 (read split allowed)
[wfmash::map] Block length min = 1500
[wfmash::map] Alphabet = DNA
[wfmash::map] Percentage identity threshold = 85%
[wfmash::map] Mapping output file = /crex/proj/uppstore2017270/Emilio/pggb/2021_08_19-late_runs/wfmash-pynVi9
[wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[wfmash::map] Execution threads  = 10
[wfmash::skch::Sketch::build] minimizers picked from reference = 16385897
[wfmash::skch::Sketch::index] unique minimizers = 6084903
[wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 3031997) ... (268, 1)
[wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 48 times during lookup.
[wfmash::map] time spent computing the reference index: 4.88354 sec
[wfmash::skch::Map::mapQuery] WARNING, no .fai index found for ./indata/completes/Ten_global_refs_cleaned.fa, reading file to sum sequence length (slow)
[wfmash::skch::Map::mapQuery] mapped 100.00% @ 5.20e+05 bp/s elapsed: 00:00:00:31 remain: 00:00:00:00
[wfmash::skch::Map::mapQuery] count of mapped reads = 9, reads qualified for mapping = 10, total input reads = 10, total input bp = 16386557
[wfmash::map] time spent mapping the query: 3.16e+01 sec
[wfmash::map] mapping results saved in: /crex/proj/uppstore2017270/Emilio/pggb/2021_08_19-late_runs/wfmash-pynVi9
[wfmash::align] Reference = [./indata/completes/Ten_global_refs_cleaned.fa]
[wfmash::align] Query = [./indata/completes/Ten_global_refs_cleaned.fa]
[wfmash::align] Mapping file = /crex/proj/uppstore2017270/Emilio/pggb/2021_08_19-late_runs/wfmash-pynVi9
[wfmash::align] Alignment identity cutoff = 8.50e-01%
[wfmash::align] Alignment output file = /dev/stdout
[wfmash::align] time spent read the reference sequences: 1.68e-07 sec
[wfmash::align::computeAlignments] aligned 100.00% @ 9.22e+05 bp/s elapsed: 00:00:01:13 remain: 00:00:00:00
[wfmash::align::computeAlignments] count of mapped reads = 10, total aligned bp = 67319873
[wfmash::align] time spent computing the alignment: 7.31e+01 sec
[wfmash::align] alignment results saved in: /dev/stdout
wfmash -X -s 500 -l 1500 -p 85 -n 9 -k 16 -t 10 ./indata/completes/Ten_global_refs_cleaned.fa ./indata/completes/Ten_global_refs_cleaned.fa
1006.17s user 28.84s system 935% cpu 110.59s total 856728Kb max memory
[seqwish::seqidx] 0.005 indexing sequences
[seqwish::seqidx] 0.232 index built
[seqwish::alignments] 0.232 processing alignments
[seqwish::alignments] 0.788 indexing
[seqwish::alignments] 2.203 index built
[seqwish::transclosure] 2.212 computing transitive closures
[seqwish::transclosure] 2.246 0.00% 0-10000000 overlap_collect
[seqwish::transclosure] 3.451 0.00% 0-10000000 rank_build
[seqwish::transclosure] 3.778 0.00% 0-10000000 parallel_union_find
[seqwish::transclosure] 4.082 0.00% 0-10000000 dset_write
[seqwish::transclosure] 4.278 0.00% 0-10000000 dset_compression
[seqwish::transclosure] 4.521 0.00% 0-10000000 dset_sort
[seqwish::transclosure] 4.622 0.00% 0-10000000 dset_invert
[seqwish::transclosure] 4.849 0.00% 0-10000000 graph_emission
[seqwish::transclosure] 4.946 92.95% 10000038-16386557 overlap_collect
[seqwish::transclosure] 5.054 92.95% 10000038-16386557 rank_build
[seqwish::transclosure] 5.147 92.95% 10000038-16386557 parallel_union_find
[seqwish::transclosure] 5.178 92.95% 10000038-16386557 dset_write
[seqwish::transclosure] 5.220 92.95% 10000038-16386557 dset_compression
[seqwish::transclosure] 5.236 92.95% 10000038-16386557 dset_sort
[seqwish::transclosure] 5.263 92.95% 10000038-16386557 dset_invert
[seqwish::transclosure] 5.287 92.95% 10000038-16386557 graph_emission
[seqwish::transclosure] 7.583 100.00% building node_iitree and path_iitree indexes
[seqwish::transclosure] 9.327 100.00% done
[seqwish::transclosure] 9.327 done with transitive closures
[seqwish::compact] 9.327 compacting nodes
[seqwish::compact] 9.881 done compacting
[seqwish::compact] 9.909 built node index
[seqwish::links] 9.909 finding graph links
[seqwish::links] 10.597 links derived
[seqwish::gfa] 10.597 writing graph
[seqwish::gfa] 13.044 done
seqwish -t 10 -s ./indata/completes/Ten_global_refs_cleaned.fa -p ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.wfmash.paf -k 19 -g ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.seqwish.gfa -B 10000000 -P
31.89s user 6.21s system 287% cpu 13.27s total 851480Kb max memory
[smoothxg::main] loading graph
[smoothxg::main] prepping graph for smoothing
[odgi::gfa_to_handle] building nodes: 100.00% @ 1.06e+06/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::gfa_to_handle] building edges: 100.00% @ 1.00e+06/s elapsed: 00:00:00:01 remain: 00:00:00:00
[odgi::gfa_to_handle] building paths: 100.00% @ 9.61e+00/s elapsed: 00:00:00:01 remain: 00:00:00:00
[smoothxg::prep] building path index
[smoothxg::prep] sorting graph
[odgi::path_linear_sgd] calculating linear SGD schedule (1.20e-11 1.00e+00 100 0 1.00e-02)
[odgi::path_linear_sgd] calculating zetas for 10028 zipf distributions
[odgi::path_linear_sgd] 1D path-guided SGD: 100.00% @ 2.71e+06/s elapsed: 00:00:01:40 remain: 00:00:00:00
[odgi::groom] grooming: 100.00% @ 2.12e+06/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::groom] organizing handles: 100.00% @ 2.12e+06/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::groom] flipped 297776 handles
[odgi::topological_order] sorting nodes: 100.00% @ 1.01e+05/s elapsed: 00:00:00:05 remain: 00:00:00:00
[smoothxg::prep] chopping graph to 100
[odgi::chop] 1459 node(s) to chop.
[smoothxg::prep] writing graph ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.seqwish.gfa.prep.gfa
[smoothxg::main] building xg index
[smoothxg::smoothable_blocks] computing blocks
[smoothxg::smoothable_blocks] computing blocks for 535041 handles: 100.00% @ 4.11e+04/s elapsed: 00:00:00:13 remain: 00:00:00:00
[smoothxg::break_and_split_blocks] cutting blocks that contain sequences longer than max-poa-length (26234) and depth >= 2000
[smoothxg::break_and_split_blocks] splitting 520 blocks at identity 0.000 (WFA-based clustering) and at estimated-identity 0.000 (mash-based clustering)
[smoothxg::break_and_split_blocks] cutting and splitting 520 blocks: 100.00% @ 4.41e+04/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::break_and_split_blocks] cut 0 blocks of which 0 had repeats
[smoothxg::break_and_split_blocks] split 0 blocks
[smoothxg::smooth_and_lace] applying global abPOA to 520 blocks: 100.00% @ 7.47e+00/s elapsed: 00:00:01:09 remain: 00:00:00:00
[smoothxg::smooth_and_lace] flipping 0 block graphs: 100.00% @ 1.34e+05/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] sorting path_mappings
[smoothxg::smooth_and_lace] adding edges from 520 graphs: 100.00% @ 6.88e+02/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] embedding 4691 path fragments: 100.00% @ 9.87e+02/s elapsed: 00:00:00:04 remain: 00:00:00:00
[smoothxg::smooth_and_lace] validating 10 path sequences: 100.00% @ 1.74e+01/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] adding nodes from 520 graphs: 100.00% @ 8.15e+01/s elapsed: 00:00:00:06 remain: 00:00:00:00
[smoothxg::smooth_and_lace] walking edges in 10 paths: 100.00% @ 7.22e+00/s elapsed: 00:00:00:01 remain: 00:00:00:00
[smoothxg::main] unchopping smoothed graph
[odgi::unchop] unchopped 332 nodes into 160 new nodes.
[smoothxg::main] smoothed graph length 2676195bp in 809019 nodes
[smoothxg::main] writing smoothed graph to ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.smooth.1.gfa
smoothxg -t 10 -T 10 -g ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.seqwish.gfa -w 118053 -K -X 100 -d 2000 -I 0 -R 0 -j 100 -e 0 -l 13117 -p 1,9,16,2,41,1 -O 0.001 -V -o ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.smooth.1.gfa
1585.78s user 91.85s system 742% cpu 225.85s total 6343400Kb max memory
[smoothxg::main] loading graph
[smoothxg::main] prepping graph for smoothing
[odgi::gfa_to_handle] building nodes: 100.00% @ 6.46e+05/s elapsed: 00:00:00:01 remain: 00:00:00:00
[odgi::gfa_to_handle] building edges: 100.00% @ 1.36e+06/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::gfa_to_handle] building paths: 100.00% @ 6.67e+00/s elapsed: 00:00:00:01 remain: 00:00:00:00
[smoothxg::prep] building path index
[smoothxg::prep] sorting graph
[odgi::path_linear_sgd] calculating linear SGD schedule (4.53e-12 1.00e+00 100 0 1.00e-02)
[odgi::path_linear_sgd] calculating zetas for 10046 zipf distributions
[odgi::path_linear_sgd] 1D path-guided SGD: 100.00% @ 3.16e+06/s elapsed: 00:00:02:23 remain: 00:00:00:00
[odgi::groom] grooming: 100.00% @ 1.62e+06/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::groom] organizing handles: 100.00% @ 3.23e+06/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::groom] flipped 308875 handles
[odgi::topological_order] sorting nodes: 100.00% @ 9.51e+04/s elapsed: 00:00:00:08 remain: 00:00:00:00
[smoothxg::prep] chopping graph to 100
[odgi::chop] 770 node(s) to chop.
[smoothxg::prep] writing graph ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.smooth.1.gfa.prep.gfa
[smoothxg::main] building xg index
[smoothxg::smoothable_blocks] computing blocks
[smoothxg::smoothable_blocks] computing blocks for 813112 handles: 100.00% @ 3.61e+04/s elapsed: 00:00:00:22 remain: 00:00:00:00
[smoothxg::break_and_split_blocks] cutting blocks that contain sequences longer than max-poa-length (26438) and depth >= 2000
[smoothxg::break_and_split_blocks] splitting 485 blocks at identity 0.000 (WFA-based clustering) and at estimated-identity 0.000 (mash-based clustering)
[smoothxg::break_and_split_blocks] cutting and splitting 485 blocks: 100.00% @ 3.95e+04/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::break_and_split_blocks] cut 0 blocks of which 0 had repeats
[smoothxg::break_and_split_blocks] split 0 blocks
[smoothxg::smooth_and_lace] applying global abPOA to 485 blocks: 100.00% @ 7.98e+00/s elapsed: 00:00:01:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] flipping 0 block graphs: 100.00% @ 6.38e+04/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] sorting path_mappings
[smoothxg::smooth_and_lace] adding edges from 485 graphs: 100.00% @ 6.43e+02/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] embedding 3758 path fragments: 100.00% @ 7.51e+02/s elapsed: 00:00:00:05 remain: 00:00:00:00
[smoothxg::smooth_and_lace] validating 10 path sequences: 100.00% @ 1.52e+01/s elapsed: 00:00:00:00 remain: 00:00:00:00
[smoothxg::smooth_and_lace] sorting consensus
[smoothxg::smooth_and_lace] embedding consensus: creating path handles
[smoothxg::smooth_and_lace] embedding consensus: creating step handles
[smoothxg::smooth_and_lace] adding nodes from 485 graphs: 100.00% @ 7.10e+01/s elapsed: 00:00:00:06 remain: 00:00:00:00
[smoothxg::smooth_and_lace] walking edges in 10 paths: 100.00% @ 8.77e+00/s elapsed: 00:00:00:01 remain: 00:00:00:00
[smoothxg::main] unchopping smoothed graph
[odgi::unchop] unchopped 154 nodes into 73 new nodes.
[smoothxg::main] smoothed graph length 2667410bp in 810120 nodes
[smoothxg::main] writing smoothed graph to ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.smooth.gfa
[smoothxg::main] building xg index from smoothed graph
terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_M_construct null not valid
Command terminated by signal 6
smoothxg -t 10 -T 10 -g ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.smooth.1.gfa -w 118971 -K -X 100 -d 2000 -I 0 -R 0 -j 100 -e 0 -l 13219 -p 1,9,16,2,41,1 -O 0.001 -Q Consensus_ -C ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.cons,1000 -o ./outdata/completes/cleaned/Ten_global_refs_cleaned.fa.adfd3d2.34ee7b1.76f53b7.smooth.gfa
1972.45s user 91.14s system 719% cpu 286.91s total 5966132Kb max memory

Thank you in advance!

[AndreaGuarracino]

Hi @emilio-r, welcome back! For some reason, some consensus paths are empty, i.e. there is not even a step in them, and this leads to the problem. So, your input is not guilty, there is a bug somewhere that is creating invalid GFAs.

[AndreaGuarracino]

This was hopefully fixed in the latest tool versions. Feel free to open it again if the problem returns!