#29 Error running ATAC in --crossspecies mode

[Dan Bolser]

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.

[Dan Bolser]

What's weird is that I've seen the -crossspecies mode run in other cases.

[Brian Walenz]

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?

[Dan Bolser]

Possible. I'll check.

[Dan Bolser]

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.