Oases\Velvet error

[mln]

Hey everyone,

I'm trying to use Oases\Velvet to make a de novo assembly, and I'm getting an error. My script is

python ./oases_pipeline.py -m 17 -M 61 -o ~project/PairedEnd -d " -fastq ~project/reads.fastq " -p " -ins_length 300 "

The error is:
assert p.returncode == 0, output[0] + "Hash failed\n" Assertionerror: Hash Failed

I'm totally stuck; any input/insight would be appreciated!

Thanks!

[mastal]

the parameter '-d' looks like it should specify the velveth command, so you probably need to specify the type of reads you have.

try adding '-shortPaired' after '-fastq' in the values for -d.

[ameng]

Hello everyone,

I'm also using oases_pipeline.py for transcriptomic analysis and I have the same kind of error :

Computer :
32 CPUs
64 Go of RAM

Data :
PE-100 / insert size unknown / 2 x 11 millions reads

Command line :
oases_pipeline.py -m 21 -M 29 -s 2 -o OASOUT -c -d ' -fastq -separate -shortPaired r1.fastq r2.fastq '

Output :
Traceback (most recent call last):
File "/home/Assembly_tools/oases_0.2.8/scripts/oases_pipeline.py", line 121, in <module>
main()
File "/home/Assembly_tools/oases_0.2.8/scripts/oases_pipeline.py", line 115, in main
singleKAssemblies(options)
File "/home/Assembly_tools/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 = 21

I've tried MAXKMERLENGTH compilation settings :
- Inscreasing 'MAXKMERLENGTH' from 31 to 71

Is that possible that this error could be due to :
- not enough RAM ?
- or something to see with the data ? since i've already succeded perfect assembly with same kind of data en parameters...

Anyone could help me ?

Thanks a lot !

[madhavi]

Hello
oases make is not working out and giving error as rm -f obj/*.o obj/dbg/*.o
cd ../velvet && make -e obj
/bin/sh: 1: cd: can't cd to ../velvet
make: *** [velvet] Error 2?
thanks

[illinu]

Hey everyone,

I'm trying to use Oases\Velvet to make a de novo assembly, and I'm getting an error. My script is

python ./oases_pipeline.py -m 17 -M 61 -o ~project/PairedEnd -d " -fastq ~project/reads.fastq " -p " -ins_length 300 "

The error is:
assert p.returncode == 0, output[0] + "Hash failed\n" Assertionerror: Hash Failed

I'm totally stuck; any input/insight would be appreciated!

Thanks!

Did you get this solved?