Xiaojun928

Thanks for your reply! I solved this problem by commenting out this line `parse_version( 'samtools --version', 1.7, qr/samtools\s(\d+\.\d+)/ms )`

Hi, Thanks for the quick response! No genome is empty in my dataset. All of them are simulated SAGs derived from isolates genomes (i.e., I randomly imported some variants ~1/10Kbp,...

Hi Dave and Matthias, For the Q2, > As script 3 (calculating the trees) was rather time-conusming, I was wondering if it’s necessary to run script 3 again, or if...

Hi Dave, Thanks for your reply. I think it's ok for me to use the current version. Another thing I want to make sure of is constructing phylogenetic trees using...

Hi Simon, Thanks for your reply! I've installed perl-autodie in the using conda. Here is a snapshot.  But I got the same output >Internal error in autodie/Fatal processing CORE::open:...

Yes, "input_sequences.fna" is in fasta/ directory, I also tried `perl Step_1_contigs_cleaning_and_gene_prediction.pl VIRSorter ./fasta ./fasta/input_sequences.fna 2` And I got the same output.

It is readable too.

I use part of scripts in wrapper_phage_contigs_sorter_iPlant.pl to generate "input_sequences.fna". Here are the scripts. ``` #!/usr/bin/perl -w use File::Spec::Functions; use File::Path 'mkpath'; my $wdir = "./"; my $input_file = "/home-user/xjwang/Minglei/double_check190731/genome_info/Roseovarius_sp_xm-a-104.genome";...

Ok, maybe I can try it on another system to see what happen. Thanks a lot!