terminate called after throwing an instance of 'std::out_of_range'

[novikk]

Getting this error on the "correcting the long reads" step:

[M::mm_idx_gen::22.928*1.52] collected minimizers
[M::mm_idx_gen::25.269*2.72] sorted minimizers
[M::main::25.270*2.72] loaded/built the index for 456779 target sequence(s)
[M::mm_mapopt_update::28.654*2.52] mid_occ = 283
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 456779
[M::mm_idx_stat::30.533*2.43] distinct minimizers: 73328105 (64.06% are singletons); average occurrences: 2.303; average spacing: 2.960
[M::worker_pipeline::294.408*7.22] mapped 456772 sequences
[M::worker_pipeline::458.370*4.73] mapped 293826 sequences
[M::mm_idx_gen::474.209*4.63] collected minimizers
[M::mm_idx_gen::475.271*4.67] sorted minimizers
[M::main::475.272*4.67] loaded/built the index for 293819 target sequence(s)
[M::mm_mapopt_update::475.272*4.67] mid_occ = 283
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 293819
[M::mm_idx_stat::475.851*4.67] distinct minimizers: 48724457 (70.21% are singletons); average occurrences: 2.138; average spacing: 2.960
[M::worker_pipeline::749.425*5.49] mapped 456772 sequences
[M::worker_pipeline::926.878*4.49] mapped 293826 sequences
[M::main] Version: 2.14-r894-dirty
[M::main] CMD: /genomics/users/irubia/tools/CONSENT/minimap2/minimap2 -k15 -w5 -m100 -g10000 -r2000 --max-chain-skip 25 --dual=yes -PD --no-long-join -t24 -I500M /genomics/users/irubia/runs/Hopkins_1_new_iso/Hopkins1.gte500.renamed.fa /genomics/users/irubia/runs/Hopkins_1_new_iso/Hopkins1.gte500.renamed.fa
[M::main] Real time: 928.346 sec; CPU: 4164.746 sec; Peak RSS: 10.984 GB
[Tue Feb 19 16:39:57 CET 2019] Correcting the long reads
terminate called after throwing an instance of 'std::out_of_range'
  what():  stoi
/genomics/users/irubia/tools/CONSENT/CONSENT-correct: line 181:  4891 Aborted                 $LRSCf/bin/CONSENT -i $tmpdir/"$PAFIndex" -a $tmpdir/"$alignments" -s "$minSupport" -S "$maxSupport" -l "$windowSize" -k "$merSize" -c "$commonKMers" -A "$minAnchors" -f "$solid" -m "$windowOverlap" -j "$nproc" -r "$reads" -M "$maxMSA" -p "$LRSCf" >> "$out"

Dataset is cDNA from the Nanopore WGS Consortium (https://github.com/nanopore-wgs-consortium/NA12878).
I filtered the dataset so that the shortest read is 500bp. Tried running with default parameters, with --windowSize 500 and --windowSize 499

[morispi]

Hi,

Dowloading the data and running ASAP.
My internet connection is pretty low at home, so can't promise I'll have the time to do it tonight.
Should be okay by tomorrow.

I'll keep you updated.

Are you running on the two datasets at once or only one of them though?

Pierre

[novikk]

Hi,

I'm running it only on Hopkins Run1 cDNA pass data, but it seems like they've merged all the runs together.

May I send you an email with the dataset?

Ivan

[morispi]

Hi,

You sure can.
My email is: pierre[dot]morisse2[at]univ-rouen[dot]fr

Pierre

[novikk]

Just sent the file via WeTransfer

[morispi]

Fixed

[novikk]

Worked perfectly, thanks!