Error when running Oases for transcriptome assembly

[yjx1217]

Hi there,

I was using oases to do the transcriptome assembly for our RNAseq data but the computation job got terminated by an error after running for 14 hrs. It seemed that oases/velvet cannot do the assembly when kmer length equals to 33 in my case (but they worked fine for k = 21 - 31). Does anyone know the reason or has a solution? Thank you very much!

The command I use to run oases is >>
/home/jy16/Programs/oases-0.2.07/scripts/oases_pipeline.py -m 21 -M 35 -o pairedEnd.diginormed -d "-fastq -shortPaired asym20h.diginormed.shuffled.fastq " -p " -ins_length 300 "

And the error message is>>

velvetg: Could not write to pairedEnd.diginormed_33/Log: No such file or directory
Traceback (most recent call last):
File "/home/jy16/Programs/oases-0.2.07/scripts/oases_pipeline.py", line 121, in <module>
main()
File "/home/jy16/Programs/oases-0.2.07/scripts/oases_pipeline.py", line 115, in main
singleKAssemblies(options)
File "/home/jy16/Programs/oases-0.2.07/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 = 33

[yjx1217]

up, any possible solution?

[kenietz]

Hi,
i got the same error for transcriptome assembly. My command line is:

oases_pipeline.py -m 21 -M 33 -s 4 -d "-shortPaired fw_reads.fastq_fasta" -p "-min_contig_lgth 500 -ins_length 290 -ins_length_sd 20" -o PE

The error is:

Traceback (most recent call last):
File "/opt/oases/oases_pipeline.py", line 121, in <module>
main()
File "/opt/oases/oases_pipeline.py", line 115, in main
singleKAssemblies(options)
File "/opt/oases/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


Have no idea whats the problem though.

[NormSci]

Try posting this problem to the Oases mailing list:

http://listserver.ebi.ac.uk/mailman/listinfo/oases-users

I believe it is run by DR Zerbino and MA Schultz, the creators of Oases and Velvet.
You'll need to sign-up for an account.

[mestato]

re-install velvet

Velvet installs automatically with a max k-mer value of 31. Reinstall it with make, setting a higher max value:
make 'MAXKMERLENGTH=70'

Velvet manual has more info.

[yjx1217]

Thank you very much, NormSci and mestato!