error happens when using sample data to test this

[zerodel]

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 ....

[bkille]

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It looks like you are using an outdated version of parsnp.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

[zerodel]

@bkille

Thanks for your reply!

I reinstalled parsnp, and now it works normally.

[zerodel]

another question.

I didn't see the vcf file.

ggr file ok tree file ok xmfa file ok ini/log , ok

[zerodel]

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 !

[zerodel]

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 !