Hello, thank you for providing such a powerful tool.
I’ve encountered a problem I can’t solve: when I use dnmtools amrfinder, it fails to produce output. At first, I thought it was a sorting problem, so I re-sorted the epiread files. This solved the issue for some samples, but for others, there’s still no output.
When I use the -v parameter, I get the following log:
AMR TESTING OPTIONS: [test=LRT] [iterations=10]
processing 1 [reads: 440292] [cpgs: 1294442]
========= POST PROCESSING =========
And then nothing else. It seems that the program didn’t actually run, rather than simply producing no positive results.
Here is my full command:
dnmtools format -f bismark -t 8 -B chr${1}.bam format${1}.bam
dnmtools states
-c Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa
-o ep${1} format${1}.bam
sort -k1,1 -k2,2n ep${1} > ep.sort${1}
dnmtools amrfinder
-c Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa
-o amr${1} ep.sort${1} -v -g 100
I’m looking forward to your reply!
Hello, thank you for providing such a powerful tool.
I’ve encountered a problem I can’t solve: when I use dnmtools amrfinder, it fails to produce output. At first, I thought it was a sorting problem, so I re-sorted the epiread files. This solved the issue for some samples, but for others, there’s still no output.
When I use the -v parameter, I get the following log:
AMR TESTING OPTIONS: [test=LRT] [iterations=10]
processing 1 [reads: 440292] [cpgs: 1294442]
========= POST PROCESSING =========
And then nothing else. It seems that the program didn’t actually run, rather than simply producing no positive results.
Here is my full command:
dnmtools format -f bismark -t 8 -B chr${1}.bam format${1}.bam
dnmtools states
-c Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa
-o ep${1} format${1}.bam
sort -k1,1 -k2,2n ep${1} > ep.sort${1}
dnmtools amrfinder
-c Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa
-o amr${1} ep.sort${1} -v -g 100
I’m looking forward to your reply!