error in Viral_Track_scanning.R

[Shiywa]

Hi, thanks for your work, I just hava a question about the Viral_Track_scanning.R. If there is no any mapping of virus, will it report an error like following?

Loading of the libraries.... ... done ! Warning message:
Output directory does not exist ! Creating it ! 
1 Fastq files are going to be processed ! 
Mapping step2_hgmm_100_R2_extracted.fastq file 
Aug 03 17:58:15 ..... started STAR run
Aug 03 17:58:15 ..... loading genome
Aug 03 17:58:26 ..... started 1st pass mapping
Aug 03 17:58:46 ..... finished 1st pass mapping
Aug 03 17:58:46 ..... inserting junctions into the genome indices
Aug 03 17:59:53 ..... started mapping
Aug 03 18:00:13 ..... finished mapping
Aug 03 18:00:16 ..... started sorting BAM
Aug 03 18:00:30 ..... finished successfully
Mapping ofstep2_hgmm_100_R2_extracted.fastq done ! 
All fastq files have been mapped successfully 
Starting the BAM file analysis 
Indexing of the bam file for step2_hgmm_100_R2_extracted is done 
Computing stat file for the bam file for step2_hgmm_100_R2_extracted is done 
Checking the mapping quality of each virus... 
Export of the viral SAM file done for step2_hgmm_100_R2_extracted 
Error in { : task 1 failed - "the condition has length > 1"
Calls: %dopar% -> <Anonymous>

[zlz6621299]

it seems that I advanced a bit, I got the QC report:

Hello, I was wondering if you have successfully run your code for COVID-19? When I aligned to the BAM file, I didn't get any correspondence for COVID-19. I've tried several datasets but still can't generate it successfully. If you have tried it, could you please send me a copy of your FASTA file (the SARS-CoV-2 reference genome)? I would like to try again after generating an index with STAR. SARS_count.txt