Closed swlong closed 8 years ago
Hi Scott, I'm not sure what's going wrong here. From the log it seems the problem is that the pileup is not being generated when new alleles are encountered. I just tried running (v0.1.5) with some local read sets, using --gene_db ARGannot.fasta and --report_new_consensus and had no errors and got expected behaviour: pileups were generated for each case where the best scoring allele was an imprecise match to the database, and consensus was extracted from this and reported in *.new_consensus_alleles.fasta output files. What version of the code are you using? I'll try a bit more trouble shooting too...
It may be a problem with the relative path and the way the cluster that I'm running it on handles it with respect to my job submission script... I'm going to take a look in the morning and see if that's the issue and if I can fix it. Thanks for taking a look for me, too.
It is a problem in the python code where it tries to prefix the supplied output on line 765. It works if the supplied output is a filename, but fails if it has directory path. I have edited the code and created a pull request to fix this issue. Thanks!
Thanks to Yunyun for sorting this out!
Thanks this is now tested and is being merged into the new release
Howdy all,
Quick question, I am trying to recover the novel allele sequences from some samples being run against the ARG database included with SRST2. I'm getting the following error when trying to create the allele pileup:
06/17/2015 12:44:06 Generate pileup... 06/17/2015 12:44:06 Running: samtools mpileup -L 1000 -f /home/mresswl/archive/ARGFinder_DB/ARGannot.fasta -Q 20 -q 1 -B data_out/KPN166ec__KPN166ec.ARGannot.sorted.bam [mpileup] 1 samples in 1 input files