segmentation fault on Nanopore data

[dominik-handler]

Hi,
when analyzing Nanopore data with NGMLR I always get these kind of errors:

NextGenMap-LR 0.2.3 (build: Feb 20 2017 11:47:16, start: 2017-02-20.13:54:24)
Contact: philipp.rescheneder@univie.ac.at
Opening for output (SAM): ~/aln_NGMLR.sam
Reading encoded reference from ~/dmel-all-chromosome-r6.12.fasta-enc.2.ngm
Reading 145 Mbp from disk took 0.04s
Reading RefTable from ~/dmel-all-chromosome-r6.12.fasta-ht-13-2.2.ngm
Reading from disk took 0.35s
Input is Fasta
Mapping reads...
Processed: 2106 (0.81), R/S: 3.30, RL: 36222, Time: 0.00 0.25 76.08, Align: 0.94, 1389, 0.93
~/run_analysis.sh: line 163: 63913 Segmentation fault      (core dumped) $NGMLR -t $NSLOTS -x ont -r $GENOMEfasta -q ${TMP}reads.fa -o ${TMP}aln_${SW}.sam

Is this a known bug and is there a fix for this?

All the best,
Dominik

[philres]

Hi Dominik,

it is not a known bug. It didn't happen on our datasets so far. However, looking at your output it seems you have much longer reads then we do in our data sets.
Is the error reproducible (does it happen with the same read when run twice) or is it just random?

[wdecoster]

I see the same/similar, on the rel3-nanopore-wgs-152889212-FAB45271.fastq.gz dataset:

ngmlr --match 3 --mismatch -7 --gap-decay 0.1 -t 15 -r genome_hg19.fa -q rel3-nanopore-wgs-152889212-FAB45271.fastq.gz -o ngm_Nanopore_human_ngmlr-0.2.3_mapped.sam
ngmlr 0.2.3 (build: Mar 30 2017 09:44:06, start: 2017-04-11.14:48:45)
Contact: philipp.rescheneder@univie.ac.at
Opening for output (SAM): ngm_Nanopore_human_ngmlr-0.2.3_mapped.sam
Encoding reference sequence.
Size of reference genome 3137 Mbp (max. 68719 Mbp)
Allocating 1568627704 (3137164016) bytes for the reference.
BinRef length: 1568627654ll (elapsed 37.691116)
0 reference sequences were skipped (length < 10).
Writing encoded reference to genome_hg19.fa-enc.2.ngm
Writing to disk took 3.85s
Building reference table
Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^31.546856)
Building RefTable #0 (kmer length: 13, reference skip: 2)
	Number of k-mers: 67108865
	Counting kmers took 274.53s
	Average number of positions per prefix: 15.558280
	58354 prefixes are ignored due to the frequency cutoff (1000)
	Index size: 335544325 byte (67108865 x 5)
	Generating index took 11.66s
	Allocating and initializing prefix Table took 4.03s
	Number of prefix positions is 855853845 (4)
	Size of RefTable is 3423415380
        Number of repetitive k-mers ignored: 371557
	Overall time for creating RefTable: 1121.14s
Writing RefTable to genome_hg19.fa-ht-13-2.2.ngm
Writing to disk took 8.01s
Input is Fastq
Mapping reads...
Processed: 57418 (0.64), R/S: 29.95, RL: 6859, Time: 16.51 4.25 51.91, Align: 0.99, 409, 0.93
Segmentation fault (core dumped)

Rerunning exactly the same produced again a segmentation error, but not on the same read:

Processed: 219468 (0.87), R/S: 66.03, RL: 7451, Time: 15.42 3.00 66.66, Align: 0.98, 471, 0.96
Segmentation fault (core dumped)

The server on which I'm working is quite busy. Would that affect this?

[philres]

Hi and thanks for your message!

I have been working on a new version (0.2.4-dev) that addresses several issues related so segmentation faults in ngmlr.

In my test runs aligning all rel3* and rel4* samples works without problems. It would be great if you could run it solves the problem for you as well. You could either pull it from the github master branch and compile it yourself or use the binary i attached to this post.
ngmlr-0.2.4-dev-beta-linux-x86_64.tar.gz

Thanks,
Philipp

[dominik-handler]

Hi, Ich hab es jezt mal für mehrere meiner Runs verwendet und hab keine Probleme mehr. Ich werd jetzt alle durch pushen und dann den Output mit Graphmap oder ähnlichem vergleichen. Danke und lg, Dominik From: Philipp Rescheneder <notifications@github.com> Reply-To: philres/ngmlr <reply@reply.github.com> Date: Wednesday, May 10, 2017 at 7:15 PM To: philres/ngmlr <ngmlr@noreply.github.com> Cc: dominik <dominik.handler@imba.oeaw.ac.at>, Author <author@noreply.github.com> Subject: Re: [philres/ngmlr] segmentation fault on Nanopore data (#10) Hi and thanks for your message! I have been working on a new version (0.2.4-dev) that addresses several issues related so segmentation faults in ngmlr. In my test runs aligning all rel3* and rel4* samples works without problems. It would be great if you could run it solves the problem for you as well. You could either pull it from the github master branch and compile it yourself or use the binary i attached to this post. ngmlr-0.2.4-dev-beta-linux-x86_64.tar.gz<https://github.com/philres/ngmlr/files/990663/ngmlr-0.2.4-dev-beta-linux-x86_64.tar.gz> Thanks, Philipp — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#10 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AL6cuYYf1tM10mvvyvI7-2F90IYTEy5Vks5r4fDFgaJpZM4MGKGS>.

[wdecoster]

It took me embarrassingly long to get back to this, but I can confirm it runs without errors now.

[philres]

Great! Thanks a lot for getting back. Wouter De Coster <notifications@github.com> schrieb am Di., 4. Juli 2017, 12:49:

…

It took me embarrassingly long to get back to this, but I can confirm it runs without errors now. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACN2HP8UCLtP_B5BmgeisQBEFwSxytnPks5sKhhfgaJpZM4MGKGS> .