Cortex error (Unable to build .unclean.kmer61.q5.ctx)

[Konstantin Chukreev]

Hello!

My question is not new, but unfortunately I didn't find any good solution in this group.

I downloaded a set of .fastq.gz sequences from an article (about 3500). The problem is that some of the runs were successful, but others (and it's rather big number of runs) have same mistake:

Unable to build /export/data/kchukreev/10_cortex/fastq/SAMEA2534104/results/binaries/uncleaned/61/SAMEA2534104.unclean.kmer61.q5.ctx at /export/home/kchukreev/soft/CORTEX_release_v1.0.5.21/scripts/calling/run_calls.pl line 2097.

Knowing that all this .fastq.gz files were generated from one source, it looks quite strange. So I want to know is it Cortex problem or not.

Kind regards,
Konstantin.

[Zamin Iqbal]

Cortex allows you to specify in advance how much memory to use. If this turns out to be not enough (eg because of noisy data or because you specified

too little by mistake), then it will fail gracefully. My guess is your failed samples had higheer sequencing error rates or coverage, and Cortex said "I need more memory".

Look in the <outdir>/binaries/uncleaned/.. directory for the failed samples, and see what the log file says