ABySS error

[thh32]

I am currently attempting to compare assemblers for use on my dataset and had set ABySS running on our cluster with the submission form :

#$ -S /bin/sh
#$ -N [running name]
#$ -e /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/ABySS_k35.error
#$ -o /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/ABySS_k35.output
#$ -M [email address]
#$ -q intel.q
#$ -cwd

module load openmpi/open64
module load abyss/1.3.7 

abyss-pe -j6 k=25 n=10 name=McCabeABySS lib='L001 L002 L003 L004 L006 L007' \
L001='McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R1_001_qualtrim.trimmed5P.fastq.oneline.matched McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R2_001_qualtrim.trimmed5P.fastq.oneline.matched' \
L002='McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R1_001_qualtrim.trimmed5P.fastq.oneline.matched McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R2_001_qualtrim.trimmed5P.fastq.oneline.matched' \
L003='McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R1_001_qualtrim.trimmed5P.fastq.oneline.matched McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R2_001_qualtrim.trimmed5P.fastq.oneline.matched' \
L004='McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R1_001_qualtrim.trimmed5P.fastq.oneline.matched McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R2_001_qualtrim.trimmed5P.fastq.oneline.matched' \
L006='McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L006_R1_001_qualtrim.trimmed5P.fastq.oneline.matched McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L006_R2_001_qualtrim.trimmed5P.fastq.oneline.matched' \
L007='McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R1_001_qualtrim.trimmed5P.fastq.oneline.matched McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R2_001_qualtrim.trimmed5P.fastq.oneline.matched'

This ran for a day and then suddenly failed, inside the .error file it stated that it had been reading the files and then discarding certain reads and then at the end had "make: *** [McCabeABySS-1.fa] Killed"

Anyone have any idea about what could have caused this? All help appreciated. The data is illumina paired end.

[GenoMax]

Did you hit a resource limit on the "intel.q" (time/memory usage/load on a node)? Any clues in the error file (ABySS_k35.error)?

[thh32]

Its unlikely that I hit a memory usage although I will look into if it could be a time issue. The full content of the .error file is:

`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R1_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 945964 reads shorter than 35 bases
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R1_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 152170 reads containing non-ACGT characters
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R2_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 715880 reads shorter than 35 bases
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R2_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 29239 reads containing non-ACGT characters
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R1_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 1042004 reads shorter than 35 bases
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R1_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 2287 reads containing non-ACGT characters
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R2_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 985348 reads shorter than 35 bases
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R2_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 4418 reads containing non-ACGT characters
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R1_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 1062278 reads shorter than 35 bases
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R1_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 17087 reads containing non-ACGT characters
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R2_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 1217657 reads shorter than 35 bases
`McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R2_001_qualtrim.trimmed5P.fastq.oneline.matched': discarded 3050 reads containing non-ACGT characters
make: *** [McCabeABySS-1.fa] Killed

[Shreyasi]

And these are the last few lines I get when I try to install abyss by typing only make:
from konnector.cc:8:
../Graph/ConstrainedBidiBFSVisitor.h: In member function ‘BFSVisitorResult ConstrainedBidiBFSVisitor<G>::checkMemLimit()’:
../Graph/ConstrainedBidiBFSVisitor.h:315:43: internal compiler error: in fold_convert_const_int_from_real, at fold-const.c:1562
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.6/README.Bugs> for instructions.
make[2]: *** [konnector-konnector.o] Error 1
make[2]: Leaving directory `/home/shreyasi/abyss-1.5.2/Konnector'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/shreyasi/abyss-1.5.2'
make: *** [all] Error 2