Comments (3)
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.
from sting.
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
from sting.
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
from sting.
Related Issues (15)
- Rewrite git history for publication
- Check licensing info HOT 1
- Automated STing MLST db
- Indexer throwing ParseError HOT 2
- subprocess.CalledProcessError HOT 5
- Proper usage of index HOT 4
- db_util.py not able to download data from PubMLST HOT 1
- Missing files HOT 2
- Could not open the input file 'ERR026529_1.fastq.gz' HOT 3
- cgMLST schemes? HOT 21
- finding rST through rMLST scheme HOT 2
- indexer reports "ERROR: The config file does not contain the [loci] section." HOT 1
- Preparing the database missing from README
- Is it possible to use assembly instead of NGS raw reads?
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