Failed to build clean binary

[Lynsey Whitacre]

Hello,

I have been using cortex_var to do variant calling on 10 samples with no reference. I split up the initial steps so that they could run parallel as follows:

[lwwvd@MUgenomics06 madtom]$ perl CORTEX_release_v1.0.5.21/scripts/calling/run_calls.pl --first_kmer 31 --last_kmer 61 -kmer_step 30 --fastaq_index index_93675 --auto_cleaning yes --bc no --pd no --outdir ./variants --ploidy 2 --genome_size 1000000000 --qthresh 5 --mem_height 25 --mem_width 100 --vcftools_dir /usr/local/bin/vcftools_0.1.12b --do_union no --logfile crtx_93675.log --workflow joint --ref Absent

For 9 of the samples this completely sucessfully. For one sample however, I get the error "Unable to build /data/lwwvd/madtom/variants/binaries/cleaned/k31/93675.kmer31.q5cleaned_6.ctx".

In the log files for 93675:

[lwwvd@MUgenomics06 k31]$ more 93675.kmer31.q5cleaned_6.ctx.log 

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Tue Jun 30 10:44:45 2015

Starting Cortex, version 1.0.5.21

Command: /data/lwwvd/madtom/CORTEX_release_v1.0.5.21//bin/cortex_var_31_c1 --kmer_size 31 --mem_height 25 --mem_width 100 --dump_binary /data/l

wwvd/madtom/variants/binaries/cleaned/k31/93675.kmer31.q5cleaned_6.ctx --remove_low_coverage_supernodes 6 --multicolour_bin /data/lwwvd/madtom/

variants/binaries/uncleaned/31/93675.unclean.kmer31.q5.ctx 

Maximum k-mer size (compile-time setting): 31

Actual K-mer size: 31

Hash table created, number of buckets: 33554432

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Tue Jun 30 10:44:45 2015

Error: Failed to read covg in db_node_read_multicolour_binary

However, in the 93675 log file in the binaries/uncleaned/31/ directory it says "Covg distribution dumped" and "Cortex completed". And in the main log file there appear to be no errors either. Also, the covg files in the binaries/uncleaned/31/ directory for sample 93675 look fine.

Any ideas what could be causing this error?

Thanks,

Lynsey

[Zamin Iqbal]

Duplicate of other email