Loading genome for test data freezes

[bostanict]

I am trying to run BatMeth2. I tried to un on mm10 but after generating the indexed genome, when I run the BatMeth2 pipel, the pipeline get stuck in this step:

==============================================================
Loading genome: ./batmeth2index/genome.fa ...

I even downloaded the test data you provided here and have the same issue:

$ BatMeth2 pipel -1 R1.fq.gz -2 R2.fq.gz -g ./batmeth2index/genome.fa -o HMD -p 30 --gff ./gene.gff
[ Program directory ] /vol/analysis/hamed/wrkdir/soft/BatMeth2/bin/
[ Program name ] BatMeth
[ Workdir ] /vol/Analysis/hamed/wrkdir/mouse/methyl/test
[ outputdir ] ./
[ BatMeth2 ] Genome: ./batmeth2index/genome.fa
[ BatMeth2 ] Annotation, gtf: ./gene.gff; bed: None;
[ BatMeth2 ] Input file:  None, R1.fq.gz R2.fq.gz
[ BatMeth2 ] Outfile prefix: HMD
[ BatMeth2 ] Process Paramater file.
[ BatMeth2 ] Process Paramater file2.
[ BatMeth2 ] Alignment ...
[ BatMeth2 ] Alignment R1.fq.gz, R2.fq.gz...
 >> ./HMD.run.log 2>&1
/vol/analysis/hamed/wrkdir/soft/BatMeth2/bin/batmeth2-align -g ./batmeth2index/genome.fa -p 30 -i R1.fq.gz -i R2.fq.g
BatMeth2 v2.00
Read length 75
Max Gap : 200
==============================================================
Loading genome: ./batmeth2index/genome.fa ...

this has been running for 8 rs on the test data and no result or error, and my ram is getting still occupied more and more. For the test data, I assume it should be pretty fast since the genome was also about 2 Mb. Could you please let me know what is going on and how I can resolve the issue?

thanks

[cosetteke]

hi, can I ask how long did it take finally?

[ZhouQiangwei]

Sorry, it's hard for me to figure out why this problem occurred. Can you try to reduce the number of threads (e.g. -p 6) to test whether it can run or download the latest version of the software through 'git clone'?