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Sheikhizadeh / pantools

PanTools
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build_pangenome shows no progress #13

Open egoltsman opened 3 years ago

egoltsman commented 3 years ago

Hello, I'm trying panTools for the first time to build a pangenome graph from 4 polished assemblies of ~70mb in size. I tried following the instructions, and the program starts, but then just sits there, spinning a cpu but not producing any output or messages. I thought that it could be related to the size of the sequences and so I tried it with a tiny test sequence but saw the same result.

java -server -jar ~/utils/PanTools/pantools-master/dist/pantools.jar build_pangenome --database_path $(pwd)/pantools.db --genomes-file foofile 

------------------------------- PanTools ------------------------------

(I wasn't sure what to pass with the --database_path flag, but my guess is that it is the name of the db to be created. ) Please let me know if I am missing something or if there is a manual page aside from the README here on github.

p.s. The java version I'm running is

openjdk 11.0.7 2020-04-14 OpenJDK Runtime Environment (build 11.0.7+10-suse-3.42.4-x8664) OpenJDK 64-Bit Server VM (build 11.0.7+10-suse-3.42.4-x8664, mixed mode)

Thank you!

egoltsman commented 3 years ago

I realized there was a typo in my command. Sorry, I fixed it, but now I'm getting an error"

java -jar ~/utils/PanTools/pantools-master/dist/pantools.jar build_pangenome -dp PanTools.db -gf genomes_file 

------------------------------- PanTools ------------------------------
WORKING_DIRECTORY = PanTools.db
PATH_TO_THE_GENOMES_FILE = genomes_file
OUTPUT_PATH has not been specified. Potential outputs will be written in PanTools.db.
Checking BdistachyonBd1_1_CHR1.fasta ...
Checking BdistachyonBd21_3_CHR1.fasta ...
Checking BdistachyonBd30_1_CHR1.fasta ...
Checking BdistachyonRef_CHR1.fasta ...
Reading BdistachyonBd1_1_CHR1.fasta ...
Reading BdistachyonBd21_3_CHR1.fasta ...
Reading BdistachyonBd30_1_CHR1.fasta ...
Reading BdistachyonRef_CHR1.fasta ...
Creating index in PanTools.db/databases/index.db/
Failed to find K!
PanTools.db/databases/index.db/sorted.kmc_pre (No such file or directory)

I tried setting -ks explicitly but got the same error. Please advise.

Thanks

avilaHugo commented 3 years ago

Hi, i'm having the same problem. If i do not declare a K size i'm prompt with: Failed to find K!

And if i declare the K-mer size : ./DB/index.db/sorted.kmc_pre (No such file or directory)