We have been trying to run VirTect to find out viral integration sites but facing some issues. We have tried to execute the sample fastq file present in Test_dataset folder along with the exact gtf file (gencode.v25.chr_patch_hapl_scaff.annotation.gtf) mentioned in your github page, human reference GRCh38.p12.genome.fa and virus database provided. We have tried running in conda environment too but getting same error. Upon running commands individually, we observed that the file generated in samtools depth step is empty. What may be the possible reason when all files mentioned in github and necessary software's are provided.
Essentially, we are looking forward to use VirTect for other vertebrates other than humans. It would be grateful if you can give us some insight that whether VirTect could be used for other species or not. Perhaps varying chromosome number and size may be a point of concern when using other organisms later.
Please provide some solution so that the execution is successful for the test dataset provided in github. For your reference I am attaching the output file. Please have a look.
Human_virtect_log.txt
Dear Authors,
We have been trying to run VirTect to find out viral integration sites but facing some issues. We have tried to execute the sample fastq file present in Test_dataset folder along with the exact gtf file (gencode.v25.chr_patch_hapl_scaff.annotation.gtf) mentioned in your github page, human reference GRCh38.p12.genome.fa and virus database provided. We have tried running in conda environment too but getting same error. Upon running commands individually, we observed that the file generated in samtools depth step is empty. What may be the possible reason when all files mentioned in github and necessary software's are provided.
Essentially, we are looking forward to use VirTect for other vertebrates other than humans. It would be grateful if you can give us some insight that whether VirTect could be used for other species or not. Perhaps varying chromosome number and size may be a point of concern when using other organisms later.
Please provide some solution so that the execution is successful for the test dataset provided in github. For your reference I am attaching the output file. Please have a look. Human_virtect_log.txt