Core dumped
pdimens opened this issue · 7 comments
Hello, I am trying to run DBG2OLC for an illumina-only assembly, and SparseAssembler seems to work correctly, outputting Contigs.txt, but I get this core dumped error when using DBG2OLC with the recommended configuration from the github page for illumina-only assembly:
Loading contigs.
703999571 k-mers in round 1.
668403631 k-mers in round 2.
Scoring method: 3
Match method: 1
Loading long read index
0 selected reads.
0 reads loaded.
./dbg1.sh: line 6: 28378 Floating point exception(core dumped) DBG2OLC LD 0 MinOverlap 31 Contigs Contigs.txt k 21 PathCovTh 2 KmerCovTh 1 i1 $FORWARD i2 $REVERSE RemoveChimera 1 ChimeraTh 2 ContigTh 2
My reads have 150x-200x coverage, and are forward+reverse. Additionally, all the software is being run in a conda environment exclusive to only DBG2OLC and its components.
Do you have any insights on what might be going on here?
The command is wrong. DBG2OLC only takes reads using f, in your command you used i1 i2.
@yechengxi Thanks for the clarification. There is no need to specify forward and reverse reads when calling DBG2OLC?
@yechengxi after taking your advice, I have rerun the DBG2OLC, and after some time processing, a different segmentation fault/core dumped issue has emerged has emerged. Are you familiar with what may be happening here?
Loading contigs.
703999571 k-mers in round 1.
668403631 k-mers in round 2.
Analyzing reads...
File1: ../../BFT_1st_R1.fastq
File2: ../../BFT_1st_R2.fastq
Long reads indexed.
Total Kmers: 93106107399
Matching Unique Kmers: 69090508968
Compression time: 333618 secs.
Scoring method: 3
Match method: 1
Loading long read index
Loading file: ReadsInfoFrom_BFT_1st_R1.fastq
1417904 bad reads skipped.
31147991 reads loaded.
Loading file: ReadsInfoFrom_BFT_1st_R2.fastq
3056832 bad reads skipped.
62046677 reads loaded.
1917738 selected reads.
62046677 reads loaded.
Average size: 2
Loaded.
1917738 reads.
Calculating reads overlaps, round 1
Multiple alignment for error correction.
./dbg1.sh: line 6: 13497 Segmentation fault (core dumped) DBG2OLC LD 0 MinOverlap 31 Contigs Contigs.txt k 21 PathCovTh 2 KmerCovTh 1 f $FORWARD f $REVERSE RemoveChimera 1 ChimeraTh 2 ContigTh 2
Please try to use one of the commands in the manual to start with.
Search for the following in the manual and you can see some examples.
Commands for Non-hybrid NGS Assembly
@yechengxi that seemed to do the trick, thank you! Does there still need to be a consensus step with blasr after the DBG2OLC step, or is this the finished illumina assembly?
Sorry for the delay. This is the finished illumina assembly.
I had sorted it out, but thank you for the repeated feedback!