Hi there,
I am having trouble with abyss-pe failing during a run. Perhaps this is a memory issue? (Although I am working on a 64 core processor with 512 MB RAM). Or perhaps a writing permissions issue?
Thanks in advance,
Andrea
Code:
nohup ~/abyss-pe np=10 k=64 name=SAF099abyss in='SAF099.1.fq SAF099.2.fq'
Here is the begin and end of the nohup.out file:
/usr/bin/mpirun -np 10 ABYSS-P -k64 -q3 --coverage-hist=coverage.hist -s abyss-bubbles.fa -o abyss-1.fa SAF099.1.fq SAF099.2.fq
ABySS 2.0.2
ABYSS-P -k64 -q3 --coverage-hist=coverage.hist -s abyss-bubbles.fa -o abyss-1.fa SAF099.1.fq SAF099.2.fq
Running on 10 processors
8: Running on host purves
9: Running on host purves
0: Running on host purves
0: Reading `SAF099.1.fq'...
1: Running on host purves
1: Reading `SAF099.2.fq'...
........................................
Pruned 3273 k-mer in 2030 tips.
Pruning tips shorter than 4 bp...
7: Pruned 259 tips.
4: Pruned 267 tips.
2: Pruned 277 tips.
10: Pruned 276 tips.
3: Pruned 280 tips.
11: Pruned 281 tips.
6: Pruned 255 tips.
8: Pruned 254 tips.
5: Pruned 295 tips.
0: Pruned 271 tips.
1: Pruned 290 tips.
9: Pruned 291 tips.
Pruned 9315 k-mer in 3296 tips.
Pruning tips shorter than 8 bp...
/data/mcfadden/aquattrini/PROGRAMS/abyss-2.0.2/bin/bin/abyss-pe:501: recipe for target 'abyss-1.fa' failed
make: *** [abyss-1.fa] Error 1