Hello!
I was running Oases/Velvet with this command
python /home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py -m 35 -M 45 -s 2 -o '/naslx/projects/uj502/di29kiz/oases/LA2750' -d '-fastq -shortPaired -separate /naslx/projects/uj502/di29kiz/libraries/NG-7404_LA2750tpool1p.fastq /naslx/projects/uj502/di29kiz/libraries/NG-7404_LA2750tpool2p.fastq' -p '-ins_length 229'
but I got this error
velvetg: Can't calloc 18446744071712318997 Annotations totalling 18446744041753829712 bytes: Cannot allocate memory
Traceback (most recent call last):
File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 121, in <module>
main()
File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 115, in main
singleKAssemblies(options)
File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 43, in singleKAssemblies
assert p.returncode == 0, "Velvetg failed at k = %i\n%s" % (k, output[0])
AssertionError: Velvetg failed at k = 35
[0.000001] Reading roadmap file /naslx/projects/uj502/di29kiz/oases/LA2750_35/Roadmaps
I have around 350 million paired reads. I'm working on a cluster that uses SLURM. Any recommendations? What should I do?
I was running Oases/Velvet with this command
python /home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py -m 35 -M 45 -s 2 -o '/naslx/projects/uj502/di29kiz/oases/LA2750' -d '-fastq -shortPaired -separate /naslx/projects/uj502/di29kiz/libraries/NG-7404_LA2750tpool1p.fastq /naslx/projects/uj502/di29kiz/libraries/NG-7404_LA2750tpool2p.fastq' -p '-ins_length 229'
but I got this error
velvetg: Can't calloc 18446744071712318997 Annotations totalling 18446744041753829712 bytes: Cannot allocate memory
Traceback (most recent call last):
File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 121, in <module>
main()
File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 115, in main
singleKAssemblies(options)
File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 43, in singleKAssemblies
assert p.returncode == 0, "Velvetg failed at k = %i\n%s" % (k, output[0])
AssertionError: Velvetg failed at k = 35
[0.000001] Reading roadmap file /naslx/projects/uj502/di29kiz/oases/LA2750_35/Roadmaps
I have around 350 million paired reads. I'm working on a cluster that uses SLURM. Any recommendations? What should I do?
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