error happens when using sample data to test this
zerodel opened this issue · comments
I tried this tool
parsnp -g ../data/ref.gb -c -d ./single_fa -c -o parsnp_out
and get error message :
The following command failed:/tmp/_MEINReRdi/parsnp parsnp_out/parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
then I tried this on sample mers data ,
parsnp -r ./ref/England1.fna -d ./genomes -c
then get error message as following:
ERROR: genome sequence Jeddah_2014_C7569.fna seems to aligned! remove and restart
no idea what happens ....
Hi @zerodel
It looks like you are using an outdated version of parsnp. The sequence Jeddah_2014_C7569.fna has inserts (-) in it and the old version of parsnp gives up when it sees this, as in your case. This has been fixed in the current version of parsnp, though. See below:
|--Parsnp 1.5.3--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
19:09:24 - INFO -
****************************************************************************************
SETTINGS:
|-refgenome: examples/mers_virus/ref/England1.fna
|-genomes:
examples/mers_virus/genomes/Al-Hasa_1_2013.fna
examples/mers_virus/genomes/Al-Hasa_12_2013.fna
...43 more file(s)...
examples/mers_virus/genomes/Taif_1_2013.fna
examples/mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna
|-aligner: muscle
|-outdir: /home/Users/blk6/Projects/HarvestSuite/parsnp/P_2020_09_15_190924438670
|-OS: Linux
|-threads: 1
****************************************************************************************
19:09:24 - INFO - <<Parsnp started>>
19:09:24 - INFO - No genbank file provided for reference annotations, skipping..
19:09:24 - WARNING - Genome sequence examples/mers_virus/genomes/Al-Hasa_4_2013.fna seems to be aligned! Skip!
19:09:24 - ERROR - File examples/mers_virus/genomes/Al-Hasa_ALL.fna is 8.91x longer than reference! Skipping...
19:09:24 - INFO - Recruiting genomes...
19:09:25 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner...
19:09:25 - INFO - Reconstructing core genome phylogeny...
19:09:30 - INFO - Aligned 46 genomes in 1.34 seconds
19:09:30 - INFO - Parsnp finished! All output available in /home/Users/blk6/Projects/HarvestSuite/parsnp/P_2020_09_15_190924438670
another question.
I didn't see the vcf file.
ggr file ok
tree file ok
xmfa file ok
ini/log , ok
It shows that, parsnp will do output validation at the end of the processing step.
https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html
~/bin/parsnp -r ~/project/parsnp/examples/mers_virus/ref/England1.fna -d ~/project/parsnp/examples/mers_virus/genomes -c -o ./out
I get
|--Parsnp 1.5.3--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
17:42:26 - INFO -
SETTINGS:
|-refgenome: /home/zerodel/project/parsnp/examples/mers_virus/ref/England1.fna
|-genomes:
/home/zerodel/project/parsnp/examples/mers_virus/genomes/Al-Hasa_12_2013.fna
/home/zerodel/project/parsnp/examples/mers_virus/genomes/Al-Hasa_15_2013.fna
...42 more file(s)...
/home/zerodel/project/parsnp/examples/mers_virus/genomes/Taif_1_2013.fna
/home/zerodel/project/parsnp/examples/mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna
|-aligner: muscle
|-outdir: ./out
|-OS: Linux
|-threads: 1
17:42:26 - INFO - <>
17:42:26 - INFO - No genbank file provided for reference annotations, skipping..
17:42:26 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner...
17:42:27 - INFO - Reconstructing core genome phylogeny...
17:42:29 - INFO - Aligned 47 genomes in 0.50 seconds
17:42:29 - INFO - Parsnp finished! All output available in ./out
Thanks in advance !
ok, seem that parsnp now use harvestools to convert .ggr file into vcf.
maybe it's better to add it to readme.
Still thanks for this tool , it helps me a lot !