Profile file for cgMLST about sting

[ar0ch]

Hey Lee, I can pull out an example this evening but to unblock you asap the profile file needs to minimally have two lines that looks like:

ST loci1 loci2 ... lociN
1 1 1 ... 1

Which is just a single dummy ST with allele 1 for all loci.

[lskatz]

Ok I bashed it out a bit with those instructions. Thanks for that clarity. Here are the steps I took after the perl -lane step.

numLoci=$(\ls -f1 *.fasta | wc -l)
(
  echo -ne "ST\t"; 
  grep -B 999999 'profile' config.txt | grep -v profile | tail -n +2 | cut -f 1 | tr '\n' '\t'; 
  echo;
) > profile.txt
(for i in `seq 1 $numLoci`; do echo -ne "1\t"; done; echo) >> profile.txt
indexer -c config.txt

It seemed to be working but I ran into a segmentation fault. What do you think?

...
8548    00040264        49      ./INNUENDO_cgMLST-00040264.fasta
8549    00040265        30      ./INNUENDO_cgMLST-00040265.fasta
8550    00040266        144     ./INNUENDO_cgMLST-00040266.fasta
8551    00040267        21      ./INNUENDO_cgMLST-00040267.fasta
8552    00040268        35      ./INNUENDO_cgMLST-00040268.fasta
8553    00040269        12      ./INNUENDO_cgMLST-00040269.fasta
8554    00040270        33      ./INNUENDO_cgMLST-00040270.fasta
8555    00040271        105     ./INNUENDO_cgMLST-00040271.fasta
8556    00040272        71      ./INNUENDO_cgMLST-00040272.fasta
8557    00040273        38      ./INNUENDO_cgMLST-00040273.fasta
8558    00040274        50      ./INNUENDO_cgMLST-00040274.fasta

Total sequences loaded: 2898302

Segmentation fault

[lskatz]

I ran time to see if memory or something might be an issue and I guess it is saying it didn't take too much. Just about 7G.

\time index -c config.txt

24.62user 6.63system 0:38.31elapsed 81%CPU (0avgtext+0avgdata 7153812maxresident)k
0inputs+0outputs (0major+1767315minor)pagefaults 0swaps