genomes in directory not used?
maguileraf opened this issue · 3 comments
maguileraf commented
I have 100 genomes in my directory but parsnp only analyzes 8 and I can't figure out why.
bkille commented
Hi @maguileraf,
Can you provide some more details? Please provide the full Parsnp command used as well as all output, for example:
blk6@sno:~/Projects/HarvestSuite/parsnp$ ./parsnp -r! -d examples/mers_virus/genomes/*.fna --out mers_demo
|--Parsnp 1.5.6--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
Ref !
13:39:38 - INFO -
**************************
SETTINGS:
|-refgenome: autopick
|-genomes:
examples/mers_virus/genomes/Al-Hasa_1_2013.fna
examples/mers_virus/genomes/Al-Hasa_12_2013.fna
...44 more file(s)...
examples/mers_virus/genomes/Taif_1_2013.fna
examples/mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna
|-aligner: muscle
|-outdir: mers_demo
|-OS: Linux
|-threads: 1
**************************
13:39:38 - INFO - <<Parsnp started>>
13:39:38 - INFO - No genbank file provided for reference annotations, skipping..
13:39:38 - ERROR - File examples/mers_virus/genomes/Al-Hasa_ALL.fna is 8.92x longer than reference! Skipping...
13:39:38 - INFO - Recruiting genomes...
13:39:39 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner...
13:39:39 - INFO - Reconstructing core genome phylogeny...
13:39:43 - INFO - Aligned 48 genomes in 1.43 seconds
13:39:43 - INFO - Parsnp finished! All output available in mers_demo
maguileraf commented
I used the wrong file as reference
bkille commented
Great, let me know if you have any further issues!