The seq.output of test differ depending on input.

[byeonggill]

ss.xlsx

This xlsx file consist of three seq.output.
Row 2 is your's seq.output.
Row 3 is output received seq_WGS.bam file as input
Row 4 is output received seq_1.fastq.gz and seq_2.fastq.gz file as input.
Why are the three output different?

my cmd: perl VIcaller.pl detect -d WGS -i test/seq_WGS -f .bam -s paired-end
my config
export PERL5LIB=/etc/perl:/usr/local/lib/x86_64-linux-gnu/perl/5.22.1:/usr/local/share/perl/5.22.1:/usr/lib/x86_64-linux-gnu/perl5/5.22:/usr/share/perl5:/usr/lib/x86_64-linux-gnu/perl/5.22:/usr/share/perl/5.22:/usr/local/lib/site_perl:/usr/lib/x86_64-linux-gnu/perl-base
export PATH=$PATH:/data/program/bowtie2/bowtie2-2.2.9/
human_genome = /data/program/VIcaller_v1.1/Database/Human/hg38.fa
human_genome_tophat = /data/program/VIcaller_v1.1/Database/Human/hg38.fa
virus_genome = /data/program/VIcaller_v1.1/Database/Virus/virus_db_090217.fa
virus_taxonomy = /data/program/VIcaller_v1.1/Database/Virus/virus_db_090217.taxonomy
virus_list = /data/program/VIcaller_v1.1/Database/Virus/virus_db_090217.virus_list
vector_db = /gpfs2/dli5lab/CAVirus/Database/Vector/Vector.fa
cell_line = /data/program/VIcaller_v1.1/Database/cell_line.list
# bowtie_d = /data/program/bowtie2/bowtie2-2.2.9/
# tophat_d = /data/program/tophat/tophat-2.1.0.Linux_x86_64/
# bwa_d = /data/program/bwa/bwa/
# samtools_d = /data/program/samtools/samtools-1.9/
# repeatmasker_d = /data/program/RepeatMasker/
# meme_d = /data/program/meme/
# NGSQCToolkit_d = /data/program/NGS_QC_Toolkit/
# fastuniq_d = /data/program/FastUniq/
# SE_MEI_d = /data/program/VIcaller_v1.1/Tools/SE-MEI/
# hydra_d = /data/program/Hydra-Version-0.5.3/
# blat_d = /home/hikim/bin/x86_64/
# blastn_d = /data/program/blast/ncbi-blast-2.5.0+

[xunchen85]

It is mainly because of the different human reference genome builds.

The test output file (Row 2 in the excel) and the input file in BAM format (test_WGS.bam) (Row 3 in the excel) are based on the hg19 reference sequence.

Hopefully it is helpful.

[byeonggill]

thanks for answer!

[xunchen85]

It results in the mistake of your config file specifying $vector_db. There should be a space between # and vector_db. Xun From: byeonggill Sent: Wednesday, April 10, 2019 3:47 AM To: xunchen85/VIcaller Cc: Xun Chen; Comment Subject: Re: [xunchen85/VIcaller] The seq.output of test differ depending oninput. (#1) thanks you for answer. I have another question about running tools. I think maybe VIcaller.pl line 396 do not run my system. but, this code run normally, if typing the command manually. This is Vicaller.pl code. This is my log files. Line 472: fail to locate the index files. but I have Vector.fa and bwa indexing file. This is my config This is Vector.fa — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[byeonggill]

I've just seen the answer.
I revised my config($vector_db)
It was my mistake.

but I have another problems.

please see the #2

thanks you!