alekseyzimin
commented
5 years ago Hi,
This is buffer overflow in ufasta split command. Can you check if everything compiled properly? Can you test "ufasta split" command, it simply splits the fasta file into several files.
Aleksey
On Thu, Jan 10, 2019, 7:01 PM Matthew Moscou <notifications@github.com wrote:
Dear @alekseyzimin https://github.com/alekseyzimin,
We are assembling a heterozygous 800 Mb plant genome with 100x Illumina PE
- 40x ONT data using MaSuRCA 3.3.0 on Ubuntu . We encountered the following error during the Gap consensus step. Having looked through issues raised by others, I believe this is a different error than described in Issue #58 https://github.com/alekseyzimin/masurca/issues/58, as mummer appears to be installed correctly. Attempting the PATH specification by JFsanchezherrero in install.sh did not correct problem. The server it is running on was a completely clean machine.
[Tue Jan 1 20:48:32 UTC 2019] Processing pe library reads [Tue Jan 1 20:48:32 UTC 2019] Average PE read length 150 [Tue Jan 1 20:48:34 UTC 2019] Using kmer size of 99 for the graph [Tue Jan 1 20:48:34 UTC 2019] MIN_Q_CHAR: 33 [Tue Jan 1 20:48:34 UTC 2019] Estimated genome size: 1165707713 [Tue Jan 1 20:48:34 UTC 2019] Creating k-unitigs with k=99 [Tue Jan 1 23:53:51 UTC 2019] Computing super reads from PE [Wed Jan 2 04:29:27 UTC 2019] Using CABOG from /home/ubuntu/canu/src/MaSuRCA-3.3.0/bin/../CA8/Linux-amd64/bin [Wed Jan 2 04:29:27 UTC 2019] Running mega-reads correction/assembly [Wed Jan 2 04:29:27 UTC 2019] Using mer size 15 for mapping, B=15, d=0.02 [Wed Jan 2 04:29:27 UTC 2019] Estimated Genome Size 1165707713 [Wed Jan 2 04:29:27 UTC 2019] Estimated Ploidy 1 [Wed Jan 2 04:29:27 UTC 2019] Using 96 threads [Wed Jan 2 04:29:27 UTC 2019] Output prefix mr.41.15.15.0.02 [Wed Jan 2 04:29:27 UTC 2019] Using 25x of the longest ONT reads [Wed Jan 2 04:37:33 UTC 2019] Reducing super-read k-mer size [Wed Jan 2 06:26:55 UTC 2019] Mega-reads pass 1 [Wed Jan 2 06:26:55 UTC 2019] Running locally in 1 batch Processed 500000 super reads, irreducible 423797, processing 264 super reads per second Processed 1000000 super reads, irreducible 813442, processing 478 super reads per second Processed 1500000 super reads, irreducible 1174760, processing 531 super reads per second Processed 2000000 super reads, irreducible 1503316, processing 627 super reads per second Processed 2500000 super reads, irreducible 1801805, processing 632 super reads per second Processed 3000000 super reads, irreducible 2084976, processing 580 super reads per second Processed 3500000 super reads, irreducible 2356970, processing 618 super reads per second Processed 4000000 super reads, irreducible 2677953, processing 570 super reads per second [Fri Jan 4 13:43:38 UTC 2019] Mega-reads pass 2 [Fri Jan 4 13:43:38 UTC 2019] Running locally in 1 batch [Thu Jan 10 21:42:47 UTC 2019] Refining alignments [Thu Jan 10 22:13:57 UTC 2019] Joining [Thu Jan 10 23:37:37 UTC 2019] Gap consensus buffer overflow detected : /home/ubuntu/canu/src/MaSuRCA-3.3.0/bin/ufasta terminated /home/ubuntu/canu/src/MaSuRCA-3.3.0/bin/mega_reads_assemble_cluster.sh: line 659: 1657 Aborted (core dumped) $MYPATH/ufasta split -i refs.renamed.fa ${ref_names[@]} Error: Failed to open reference file 'to_join.3.fa' Usage: nucmer [options] ref:path qry:path+ Use --help for more information Error: Failed to open reference file 'to_join.1.fa'
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/alekseyzimin/masurca/issues/87, or mute the thread https://github.com/notifications/unsubscribe-auth/AZ9zHY3rEvHKuMYRGRG1LjiMEkCjeLOtks5vB9Q-gaJpZM4Z6jLa .
matthewmoscou
gmarcais
estolle
Dear @alekseyzimin,
We are assembling a heterozygous 800 Mb plant genome with 100x Illumina PE + 40x ONT data using MaSuRCA 3.3.0 on Ubuntu . We encountered the following error during the Gap consensus step. Having looked through issues raised by others, I believe this is a different error than described in Issue #58, as mummer appears to be installed correctly. Attempting the PATH specification by JFsanchezherrero in install.sh did not correct problem. The server it is running on was a completely clean machine.