16435 Segmentation fault during pregraph step

[AllisonStander]

Hi there,

Could someone please give some information on the following error:

/var/spool/PBS/mom_priv/jobs/1701598.sched01.SC: line 18: 16435 Segmentation fault

In the other error file:

---

Pregraph

---

Parameters: pregraph -s /home/astander2/lustre/00_GenomeRooibos/05_FullRuns/01_SOAPdenovo2/00_LargeSubset/00_ConfigFile.txt -K 53 -p 56 -R -o SOAPK53_LargeSub.graph

In /home/astander2/lustre/00_GenomeRooibos/05_FullRuns/01_SOAPdenovo2/00_LargeSubset/00_ConfigFile.txt, 3 lib(s), maximum read length 125, maximum name length 256.

56 thread(s) initialized.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/L5R1n_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/L5R2n_p.fastq.gz
--- 100000000th reads.
--- 200000000th reads.
--- 300000000th reads.
--- 400000000th reads.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/L6R1n_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/L6R2n_p.fastq.gz
--- 500000000th reads.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L1R1_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L1R2_p.fastq.gz
--- 600000000th reads.
--- 700000000th reads.
--- 800000000th reads.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L2R1_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L2R2_p.fastq.gz
--- 900000000th reads.
--- 1000000000th reads.
--- 1100000000th reads.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L3R1s17_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L3R2s17_p.fastq.gz
--- 1200000000th reads.
--- 1300000000th reads.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L4R1_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/S1L4R2_p.fastq.gz
--- 1400000000th reads.
--- 1500000000th reads.
--- 1600000000th reads.
--- 1700000000th reads.
Time spent on hashing reads: 14372s, 1743581530 read(s) processed.
LIB(s) information:
[LIB] 0, avg_ins 300, reverse 0.
[LIB] 1, avg_ins 3000, reverse 1.
[LIB] 2, avg_ins 8000, reverse 1.
31381462521 node(s) allocated, 118774619742 kmer(s) in reads, 118774619742 kmer(s) processed.
done hashing nodes
29884555734 linear node(s) marked.
Time spent on marking linear nodes: 361s.
Time spent on pre-graph construction: 14734s.

Start to remove frequency-one-kmer tips shorter than 106.
Total 734662439 tip(s) removed.
56 thread(s) initialized.
333566414 linear node(s) marked.
Start to remove tips with minority links.
49302346 tip(s) removed in cycle 1.
160412 tip(s) removed in cycle 2.
599 tip(s) removed in cycle 3.
1 tip(s) removed in cycle 4.
0 tip(s) removed in cycle 5.
Total 49463358 tip(s) removed.
56 thread(s) initialized.
0 linear node(s) marked.
Time spent on removing tips: 31000s.

--- 10000000 edge(s) built.
--- 20000000 edge(s) built.
--- 30000000 edge(s) built.
--- 40000000 edge(s) built.
--- 50000000 edge(s) built.
--- 60000000 edge(s) built.
--- 70000000 edge(s) built.
--- 90000000 edge(s) built.
--- 150000000 edge(s) built.
--- 160000000 edge(s) built.
--- 180000000 edge(s) built.
--- 220000000 edge(s) built.
--- 230000000 edge(s) built.
--- 280000000 edge(s) built.
--- 300000000 edge(s) built.
--- 310000000 edge(s) built.
--- 330000000 edge(s) built.
--- 340000000 edge(s) built.
--- 350000000 edge(s) built.
--- 360000000 edge(s) built.
--- 380000000 edge(s) built.
--- 440000000 edge(s) built.
--- 450000000 edge(s) built.
494087158 (247046261) edge(s) and 47488856 extra node(s) constructed.
Time spent on constructing edges: 7811s.

In file: /home/astander2/lustre/00_GenomeRooibos/05_FullRuns/01_SOAPdenovo2/00_LargeSubset/00_ConfigFile.txt, max seq len 125, max name len 256.
56 thread(s) initialized.
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/L5R1n_p.fastq.gz
Import reads from file:
/home/astander2/lustre/00_GenomeRooibos/03_CleanNoFBT/00_PairedFiles/L5R2n_p.fastq.gz

Any information on what may be causing this, would be much appreciated.

Regards,
Allison