Error running ATAC in --crossspecies mode
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florea
I'm getting the following error when trying to run ATAC in crossspecies mode.
Here is my command line:
atac.pl -meryldir /tmp/atac_meryl_4o45PJ -dir /tmp/atac_out__xyZQo -id1 sequence1 -seq1 solanum_lycopersicum.fasta.leaff -id2 sequence2 -seq2 solanum_tuberosum.fasta.leaff -crossspecies
Which gives this output:
/path/meryl -B -C -threads 2 -m 18 -s /tmp/atac_meryl_4o45PJ/sequence1.fasta -o /tmp/atac_meryl_4o45PJ/sequence1.ms18 /path/meryl -v -M lessthanorequal 9 -s /tmp/atac_meryl_4o45PJ/sequence1.ms18 -o /tmp/atac_meryl_4o45PJ/sequence1.ms18.le9 /path/meryl -B -C -threads 2 -m 18 -s /tmp/atac_meryl_4o45PJ/sequence2.fasta -o /tmp/atac_meryl_4o45PJ/sequence2.ms18 /path/meryl -v -M lessthanorequal 9 -s /tmp/atac_meryl_4o45PJ/sequence2.ms18 -o /tmp/atac_meryl_4o45PJ/sequence2.ms18.le9 Finding the min count between sequence1.ms18.le9 and sequence2.ms18.le9. /path/meryl -M min -s /tmp/atac_meryl_4o45PJ/sequence1.ms18.le9 -s /tmp/atac_meryl_4o45PJ/sequence2.ms18.le9 -o /tmp/atac_out__xyZQo/work/min.sequence1.ms18.le9.sequence2.ms18.le9 includeSize is proportional to 426669776. excludeSize is proportional to 1736031168. /tmp/atac_out__xyZQo/work/min.sequence1.ms18.le9.sequence2.ms18.le9 has 109005735 mers. /tmp/atac_meryl_4o45PJ/sequence1.ms18 has 737178106 mers. includeSize is exactly 109005735 mers. excludeSize is exactly 628172371 mers. /path/seatac -verbose -mersize 18 -minlength 18 -maxgap 0 -numthreads 4 -table /tmp/atac_meryl_4o45PJ/sequence1.fasta -stream /tmp/atac_meryl_4o45PJ/sequence2.fasta -only /tmp/atac_out__xyZQo/work/sequence1vssequence2.include -output /tmp/atac_out__xyZQo/work/sequence1vssequence2-segment-000.matches -filtername /path/../lib/filter-heavychains.so -filteropts "-1 sequence1 -2 sequence2 -S 100 -J 100000" > /tmp/atac_out__xyZQo/work/sequence1vssequence2-000.out 2>&1 /path/matchExtender -e 4 -b 5 -s 5 -i 0.70 -p 100 -d 25 /tmp/atac_out__xyZQo/work/sequence1vssequence2.header /tmp/atac_out__xyZQo/work/sequence1vssequence2-segment-000.matches > /tmp/atac_out__xyZQo/work/sequence1vssequence2.matches.extended seqFactory::registerFile()-- Cannot determine type of file ''. Tried: seqFactory::registerFile()-- 'FastAstream' seqFactory::registerFile()-- 'FastA' seqFactory::registerFile()-- 'Fastq' seqFactory::registerFile()-- 'seqStore' Failed.
What's weird is that I've seen the -crossspecies mode run in other cases.
The error message is indicating the name of the file isn't set. The filenames are supposed to be in the header of the 'atac' files - I'd guess it's in the *header file in the command. Any chance /tmp filled up?
Possible. I'll check.
A mere 18Tb free on that device, so I don't think that's the issue. Unfortunately, I lost the header file. I'll have to re-run.