Result_visual3-3.pl ERROR

[junyanzho]

Dear Developer, I encounter a error while run VIcaller, error message “Modification of non-creatable array value attempted, subscript -1 at Result_visual3-3.pl”

When I looked into the script “Result_visual3-3.pl” , I found that input file “$ARGV[0]_sf.fuq” maybe not exist in any scripts.

Could you help me check it?

Thanks! JY

[xunchen85]

Hi JY,

Did you have "${sample}_sf.fuq" file after your running VIcaller? Can you show me the list of files you currently have?

Best, Xun

[junyanzho]

Hi, xunchen

After run VIcaller, 3 files with suffix 'fuq': ${sample}_1.1fuq, ${sample}_2.1fuq, ${sample}_1sf.fuq. I try to step by step run, and found the file ${sample}_sf.fuq is not exist.

[junyanzho]

Hi, xunchen, VIcaller generate files as below show(by time): sample_pe.bam sample_soft.fastq.gz sample_h1.sort.bam sample_h1_1.1fq sample_h1_2.1fq sample_h1_h.bam sample_su.bam sample_sm.bam sample_h1_pe.bam sample_h1_soft.fastq.gz sample_h1_h1.sort.bam sample_1sf.fastq IlluQC_Filtered_files sample_1.1fq sample_2.1fq sample_vsu.sort.bam sample_vsoft_sort.bam sample.type sample_In.virus_v3 sample_1.1fuq sample_2.1fuq sample_1sf.fuq sample_1sf.othu sample.3 sample.error sample_f2 sample.virus_f sample.virus_f2 sample.visualization sample.fine_mapped sample_vector.sam sample_vector.hmap sample_vector.hunmapped sample_vector_sf.sam sample_vector_sf.hmap sample_vector_sf.hunmapped sample_vector.hmapped sample.output

Thanks a lot JY

[xunchen85]

Hi JY,

Thanks for pointing it out. The file name in the script should be changed to "1sf.fuq". It will only impact the read visualization but not viral integrations detection.

I have revised the corresponding script.

Thanks, Xun

[junyanzho]

Hi xunchen,

Thank you for your reply and help. I have another question about virus genome. For HBV integration detection, can I just take HBV genome as virus reference? Simply extract information of HBV reference NC_003977.1 from files virus_db_090217.fa, virus_db_090217.taxonomy and virus_db_090217.virus_list as a custom reference.

Best, JY

[xunchen85]

Yes if you change the viral database and taxonomy information consistently.

Best, Xun