Hello,
- I am running "velvet".
- Velvet that I am using is the latest version.
- After running velvetg, I've got error message "segmentation fault".
- I think the memory is enough: I can use either 768 GB or 128 GB machine.
The commands that I used are the below.
556825727 sequences found
...
[107491.832312] Inputting sequence 556000000 / 556825727
[107637.486093] === Sequences loaded in 104746.688101 s
[107637.491597] Done inputting sequences
[107637.491604] Destroying splay table
[107650.200950] Splay table destroyed
srun: error: node92: task 0: Segmentation fault
I've got this error message. Would you please give me a piece of advice to resolve my problem? Thank you in advance.
- I am running "velvet".
- Velvet that I am using is the latest version.
- After running velvetg, I've got error message "segmentation fault".
- I think the memory is enough: I can use either 768 GB or 128 GB machine.
The commands that I used are the below.
make 'CATEGORIES=4'
srun -p bigmem ./velveth OUTPUT_1 31 -fastq -shortPaired 02_L7.fastq 02_L8.fastq -fastq -shortPaired2 05_L7.fastq 05_L8.fastq -fastq -shortPaired3 08_L7.fastq 08_L8.fastq -fastq -shortPaired4 11_L7.fastq 11_L8.fastq > output1.out 2>&1 &
...
[107491.832312] Inputting sequence 556000000 / 556825727
[107637.486093] === Sequences loaded in 104746.688101 s
[107637.491597] Done inputting sequences
[107637.491604] Destroying splay table
[107650.200950] Splay table destroyed
srun -p bigmem -c 16 ./velvetg OUTPUT_1 -read_trkg yes -amos_file yes -unused_reads yes -exp_cov 10 -ins_length 3000 -ins_length_sd 1000 -ins_length2 6000 -ins_length_sd 1000 -ins_length3 9000 -ins_length_sd 1000 -ins_length4 11000 > output1_g.out 2>&1 &
I've got this error message. Would you please give me a piece of advice to resolve my problem? Thank you in advance.
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