Failed to find alternate path

[mbhall88]

https://github.com/rmcolq/pandora/blob/565c1572f2c535db20c45062d359055d04a7659a/src/localPRG.cpp#L1406-L1407

I've triggered this error and don't really know why/how? Any suggestions on how to get to the bottom of this @leoisl?

I have created a minimal dataset to reproduce this in /hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map

Inside that directory, if you run pandora (v0.9.1 prebuilt binary - /hps/nobackup/iqbal/mbhall/drprg/src/ext/pandora) like so, you will get the error

cd /hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map
/hps/nobackup/iqbal/mbhall/drprg/src/ext/pandora map -k 15 -w 15 --genotype -v -o . -g 4.4m --vcf-refs gyrA.fa -t 1 gyrA.prg mada_118.sub.fq.gz

And the log

[2022-07-15 05:17:04.163752] [0x0000000000e32940] [info]    Loading Index and LocalPRGs from file...
[2022-07-15 05:17:04.163765] [0x0000000000e32940] [debug]   Loading index
[2022-07-15 05:17:04.163771] [0x0000000000e32940] [debug]   File is "/hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map/gyrA.prg.k15.w15.idx"
[2022-07-15 05:17:04.166459] [0x0000000000e32940] [debug]   Finished loading file. Index now contains 472 entries
[2022-07-15 05:17:04.166468] [0x0000000000e32940] [debug]   Loading PRGs from file "/hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map/gyrA.prg"
[2022-07-15 05:17:04.169743] [0x0000000000e32940] [debug]   Number of LocalPRGs read: 1
[2022-07-15 05:17:04.169751] [0x0000000000e32940] [debug]   Loading kmer_prgs from files
[2022-07-15 05:17:04.178086] [0x0000000000e32940] [info]    Constructing pangenome::Graph from read file (this will take a while)...
[2022-07-15 05:17:12.736064] [0x0000000000e32940] [info]    Processed 23726 reads
[2022-07-15 05:17:12.736083] [0x0000000000e32940] [debug]   Pangraph has 1 nodes
[2022-07-15 05:17:12.736086] [0x0000000000e32940] [debug]   Estimated coverage: 20
[2022-07-15 05:17:12.736110] [0x0000000000e32940] [info]    Writing pangenome::Graph to file "/hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map/./pandora.pangraph.gfa"
[2022-07-15 05:17:12.742746] [0x0000000000e32940] [debug]   added node 0
[2022-07-15 05:17:12.744506] [0x0000000000e32940] [info]    Updating local PRGs with hits...
[2022-07-15 05:17:12.744926] [0x0000000000e32940] [debug]   Added 1645 hits in the forward direction and 2216 hits in the reverse
[2022-07-15 05:17:12.744931] [0x0000000000e32940] [info]    Estimating parameters for kmer graph model...
[2022-07-15 05:17:12.744940] [0x0000000000e32940] [info]    Collect kmer coverage distribution
[2022-07-15 05:17:12.744973] [0x0000000000e32940] [info]    Writing kmer coverage distribution to "/hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map/./kmer_covgs.txt"
[2022-07-15 05:17:12.751193] [0x0000000000e32940] [debug]   Found mean 10.9093
[2022-07-15 05:17:12.751202] [0x0000000000e32940] [debug]   Found variance 13.7255
[2022-07-15 05:17:12.751207] [0x0000000000e32940] [debug]   mean, var: 10.9093, 13.7255
[2022-07-15 05:17:12.751210] [0x0000000000e32940] [debug]   nb reads, covg31, 20
[2022-07-15 05:17:12.751216] [0x0000000000e32940] [debug]   Negative binomial parameters p: 0.794824 and r: 42.2613
[2022-07-15 05:17:12.751220] [0x0000000000e32940] [info]    Collect kmer probability distribution
[2022-07-15 05:17:12.751648] [0x0000000000e32940] [info]    Writing kmer probability distribution to "/hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map/./kmer_probs.txt"
[2022-07-15 05:17:12.755291] [0x0000000000e32940] [info]    Did not find enough non-zero coverage kmers to estimated threshold for true kmers. Use the naive threshold -9
[2022-07-15 05:17:12.755298] [0x0000000000e32940] [info]    Find PRG paths and write to files...
[2022-07-15 05:17:12.755306] [0x0000000000e32940] [info]    Loading VCF refs from file "/hps/nobackup/iqbal/mbhall/drprg/paper/results/drprg/wk_sweep/predict/w15/k15/nanopore/mada_118/tmp_map/gyrA.fa"
[2022-07-15 05:17:12.755767] [0x0000000000e32940] [debug]   Find maxpath for gyrA
[2022-07-15 05:17:12.755879] [0x0000000000e32940] [debug]   Found non-zero coverage in kmer graph
[2022-07-15 05:17:12.756739] [0x0000000000e32940] [debug]   Convert kmernode path to localnode path
[2022-07-15 05:17:12.756948] [0x0000000000e32940] [debug]   Found global coverage 20 and path mode 13 and mean 11
[2022-07-15 05:17:12.757169] [0x0000000000e32940] [debug]   have 1 candidates
[2022-07-15 05:17:12.757178] [0x0000000000e32940] [debug]   Build VCF for prg gyrA
[2022-07-15 05:17:12.757231] [0x0000000000e32940] [debug]   Update VCF with sample path
[2022-07-15 05:17:12.757272] [0x0000000000e32940] [debug]   Update VCF with sample covgs
terminate called after throwing an instance of 'FatalRuntimeError'
  what():  [FATAL ERROR]: Error finding alternative path: no alternative paths were found but we should have found at least one
Aborting...

DEBUG info (for developers, provide this if opening an issue):
Stack trace (most recent call last):
#11   Object "[0x42869d]", at 0x42869d, in
#10   Object "[0xaf6f7f]", at 0xaf6f7f, in
#9    Object "[0x4238ff]", at 0x4238ff, in
#8    Object "[0x51180f]", at 0x51180f, in
#7    Object "[0x504882]", at 0x504882, in
#6    Object "[0x5165ca]", at 0x5165ca, in
#5    Object "[0xadb965]", at 0xadb965, in
#4    Object "[0x514f31]", at 0x514f31, in
#3    Object "[0x4dda54]", at 0x4dda54, in
#2    Object "[0x4dcd43]", at 0x4dcd43, in
#1    Object "[0x4d944f]", at 0x4d944f, in
#0    Object "[0x4f1817]", at 0x4f1817, in

Stack trace (most recent call last):
#16   Object "[0x42869d]", at 0x42869d, in
#15   Object "[0xaf6f7f]", at 0xaf6f7f, in
#14   Object "[0x4238ff]", at 0x4238ff, in
#13   Object "[0x51180f]", at 0x51180f, in
#12   Object "[0x504882]", at 0x504882, in
#11   Object "[0x5165ca]", at 0x5165ca, in
#10   Object "[0xadb965]", at 0xadb965, in
#9    Object "[0x514f31]", at 0x514f31, in
#8    Object "[0x4089d2]", at 0x4089d2, in
#7    Object "[0xaf4979]", at 0xaf4979, in
#6    Object "[0xaf3f8a]", at 0xaf3f8a, in
#5    Object "[0xa2fd43]", at 0xa2fd43, in
#4    Object "[0xad0418]", at 0xad0418, in
#3    Object "[0xa3009b]", at 0xa3009b, in
#2    Object "[0x41f232]", at 0x41f232, in
#1    Object "[0x421c00]", at 0x421c00, in
#0    Object "[0x435b0b]", at 0x435b0b, in
Aborted (Signal sent by tkill() 1061390 7196)

Sorry I would try and debug myself but I am struggling to build pandora at the moment - something to do with SeqAn.

[leoisl]

Hey, sorry for the delay. I will try to take a look at this next week. Thanks for the bug report with a MWE, helps a lot!

[leoisl]

I am still off pandora, but will return to it soon

[leoisl]

Is this still relevant @mbhall88 ?

[mbhall88]

Maybe, but it isn't blocking me (it only happened at a certain w and k value and I'm not using those w/k values currently)