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jkimlab / GMASS

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"Error - Cannot open net dir", chainNet dir not being made #1

Open madmolecularman opened 5 years ago

madmolecularman commented 5 years ago

Hello Kim Lab,

Per your instructions I followed the quick start installation guide with these three commands:

git clone https://github.com/jkimlab/GMASS.git cd GMASS perl setup.pl install

In attempting to run the check on how the setup.pl completed install I ran the following code:

perl calculateGMASS.pl -p example/params.txt -o outdir

Here is the raw error from that run:: Input -Assembly1: /home/jgreen/GMASS/example/Assembly1.fa -Assembly2: /home/jgreen/GMASS/example/Assembly2.fa -Resolution: 10000,20000,30000,40000,50000 -Alignment strictness: near -cpu: 1

Set Assembly1.fa as reference, and Assembly2.fa as target -N50 of Assembly1.fa: 1435559 -N50 of Assembly2.fa: 1426293

Detect CSBs /home/jgreen/GMASS/build_synteny.pl --path /home/jgreen/GMASS/path.conf -c /home/jgreen/GMASS/outdir/chainNet -m 10000,20000,30000,40000,50000 -r Assembly1 -t Assembly2 -o /home/jgreen/GMASS/outdir/CSB

** Error - Could not open net dir /home/jgreen/GMASS/outdir/chainNet/Assembly1/Assembly2/net

Calculate GMASS -The CSBs was not constructed in 10000. The GMASS score will be calculated except CSB information in 10000. -The CSBs was not constructed in 20000. The GMASS score will be calculated except CSB information in 20000. -The CSBs was not constructed in 30000. The GMASS score will be calculated except CSB information in 30000. -The CSBs was not constructed in 40000. The GMASS score will be calculated except CSB information in 40000. -The CSBs was not constructed in 50000. The GMASS score will be calculated except CSB information in 50000. Illegal division by zero at calculateGMASS.pl line 346, line 180. **

I believe the error exists somewhere between line 166-171 but I might be wrong.:

my $aln_cmd = "$script_dir/whole_genome_alignment.pl --path $script_dir/path.conf -p $core -res $resolutions[0] -r $ref_fa -t $tar_fa -d $distance -o $output_dir/chainNet 2> $output_dir/aln.log"; my $bld_CSB_cmd = "$script_dir/build_synteny.pl --path $script_dir/path.conf -c $output_dir/chainNet -m $resols -r $ref_name -t $tar_name -o $output_dir/CSB";

print STDERR "$bld_CSB_cmd\n"; if(-d "$output_dir/chainNet"){ rm -rf $output_dir/chainNet; }

It seems to me that the chainNet directory is not being made or it is being removed before it can be accessed by the proper commands on 174-175

$aln_cmd; $bld_CSB_cmd;

Any assistance you can provide would be greatly appreciated. Thank you for your time.

Sincerely,

Jacob Michael Green

daeh0ng commented 5 years ago

Hello,

I think some third-party tools weren't normally installed. Please check that the following programs are normally installed and executed.

Sincerely,

Daehong Kwon

chopra29 commented 4 years ago

I ran into similar issue. I tried to install this tool again.

Thank you.

daeh0ng commented 4 years ago

Hi, Did you check that the third-party tools are installed correctly? GMASS requires the tools for building net directories and net files.

Thanks.