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yechengxi / DBG2OLC

A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.
GNU General Public License v3.0
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Segmentation fault (core dumped) when analyzing reads #49

Closed jmodlis closed 5 years ago

jmodlis commented 6 years ago

Hi, I'm trying to run dbg2olc with a small amount of nanopore data and a pre-existing assembly. It has repeatedly had a segmentation fault at the same step. If you have any insight as to what is going on, I would really appreciate it! I did run selectLongestReads before hand but it just selected all of the reads since the coverage is so low.

Thanks, Jen

Here is the command:

"$dbg2olcPATH"/./DBG2OLC k 17 AdaptiveTh 0.001 KmerCovTh 2 MinOverlap 20 MinLen 500 RemoveChimera 0 Contigs "$assembly" f "$selectedReads"

Here is the end of the outfile:

Loading contigs.
238092557 k-mers in round 1.
194244643 k-mers in round 2.
Analyzing reads...
File1: /data/processedData/dbg2olc_selectReads/nanoporeLongestReadsAllRuns.fasta
zrlewis commented 6 years ago

I am seeing a similar error, I think. Did you find a workaround? Any help would be appreciated.

Loading contigs.
20 k-mers in round 1.
19 k-mers in round 2.
Analyzing reads...
File1: PB_reads.fasta
Long reads indexed. 
Total Kmers: 157384323679
Matching Unique Kmers: 5487266
Compression time: 23756 secs.
Scoring method: 3
Match method: 2
Loading long read index
Loading file: ReadsInfoFrom_Physalia_concatenated_reads.fasta
516513 reads loaded.
/var/spool/slurmd/job25152457/slurm_script: line 13: 25169 Floating point exception(core dumped) DBG2OLC k 17 AdaptiveTh 0.01 KmerCovTh 2 MinOverlap 30 RemoveChimera 1 Contigs ContigGraph.txt f PB_reads.fasta
jmodlis commented 6 years ago

No, and I even had help from our IT department. I eventually gave up and tried links, redundans, and space-long reads instead. I think it may have something to do with the fact that my assembly was created by an external program, but that was the whole point of using a scaffolding program.

Your error has been mentioned before in the issues - you may want to check that your input command is correct.

Jen

zrlewis commented 6 years ago

@jmodlis Thanks for the update. I'm sorry that you weren't able to figure it out.

Good idea on checking my input. I think that I should have specified Contigs.txt and for some reason I put ContigGraph.txt as input. This might solve my issue.

yechengxi commented 6 years ago

The reason could be the contigs are created using an untested assembler. In that case the contigs may have unknown properties that are not suitable for DBG2OLC.