Path to paf2net.py not correct in latest Docker build

[brettChapman]

Hi

I'm trying to run partition-before-pggb with latest 0.5.4 build on Docker.

I appears the build is pointing to the wrong location for scripts.

I get this error:

srun -n 1 singularity exec --bind /data/lupin_pangenome/pggb_run:/data/lupin_pangenome/pggb_run /data/pggb_builds/pggb_v0.5.4_Fatica.sif partition-before-pggb -i /data/lupin_pangenome/pggb_run/lupin_pangenome.fasta -s 5000 -l 0 -p 97 -n 7 -k 47 -B 10000000 -P asm20 -t 32 -T 16 -V L1:#:1000 -m -A -S -Z -o lupin_pangenome_s5000_l0_p97_k47_B10000000_G700-900-1100_Pasm20
[wfmash::map] Reference = [/data/lupin_pangenome/pggb_run/lupin_pangenome.fasta]
[wfmash::map] Query = [/data/lupin_pangenome/pggb_run/lupin_pangenome.fasta]
[wfmash::map] Kmer size = 19
[wfmash::map] Window size = 213
[wfmash::map] Segment length = 5000 (read split allowed)
[wfmash::map] Block length min = 0
[wfmash::map] Chaining gap max = 50000
[wfmash::map] Percentage identity threshold = 97%
[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  = 32
[wfmash::skch::Sketch::build] minimizers picked from reference = 62129839
[wfmash::skch::Sketch::index] unique minimizers = 3965697
[wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 164401) ... (1315543, 1)
[wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 48030 times during lookup.
[wfmash::map] time spent computing the reference index: 21.9314 sec
[wfmash::skch::Map::mapQuery] mapped 100.00% @ 4.56e+06 bp/s elapsed: 00:00:24:07 remain: 00:00:00:00
[wfmash::skch::Map::mapQuery] count of mapped reads = 181, reads qualified for mapping = 182, total input reads = 182, total input bp = 6597089964
[wfmash::map] time spent mapping the query: 1.45e+03 sec
[wfmash::map] mapping results saved in: /dev/stdout
wfmash -s 5000 -l 0 -p 97 -n 6 -k 19 -H 0.001 -X -t 32 --tmp-base lupin_pangenome_s5000_l0_p97_k47_B10000000_G700-900-1100_Pasm20 /data/lupin_pangenome/pggb_run/lupin_pangenome.fasta --approx-map
40344.06s user 786.99s system 2798% cpu 1470.00s total 13161008Kb max memory
python3: can't open file '/usr/local/bin/scripts/paf2net.py': [Errno 2] No such file or directory
srun: error: node-10: task 0: Exited with exit code 2

Thanks.

[AndreaGuarracino]

Hi @brettChapman, I've just pushed a change that should fix your issue. Could you try again with the latest Docker build?

[brettChapman]

Thanks. I was able to run now to completion.