Unable to build uncleaned binaries

[Bjarne Ridderberg]

Hi Zam.

I am trying to use cortex to call variants on 16 bacterial genomes without a reference, but i keep getting this error message.

Unable to build /faststorage/project/ClinicalMicrobio/05winnie/cortex/binaries/uncleaned/32/A23255.unclean.kmer32.q5.ctx at /com/extra/cortex_var/1.0.5.21/scripts/calling/run_calls.pl line 2097

My script looks like this

perl /com/extra/cortex_var/1.0.5.21/scripts/calling/run_calls.pl --first_kmer 31 --last_kmer 61 kmer_step 30 --fastaq_index /home/wrid/ClinicalMicrobio/02winnie/INDEX --auto_cleaning yes --bc yes --pd no --outdir /home/wrid/ClinicalMicrobio/faststorage/05winnie/cortex --outvcf saureus1 --ploidy 1 --stampy_hash /home/wrid/ClinicalMicrobio/faststorage/05winnie/cortex/saureus1 --stampy_bin /com/extra/stampy/1.0.23/load.sh --genome_size 2800000 --qthresh 5 --mem_height 21 --mem_width 100 --vcftools_dir /com/extra/vcftools/0.1.12b/load.sh --do_union yes --ref Absent --workflow joint --logfile logfile,f --apply_pop_classifier

In the log-file for A23255.unclean.kmer32.q5.ctx there is no error - everything looks fine there.

I hope you can help me get past this.

Best

Winnie

[Zamin Iqbal]

Hi Winnie

what is the error message in

/faststorage/project/ClinicalMicrobio/05winnie/cortex/binaries/uncleaned/32/A23255.unclean.kmer32.q5.ctx.build_log ?

regards

Zam