Hi,
Thank you so much for the nice software. When I run the Viral_Track_scanning.R a error were present as follows;
Loading of the libraries.... ... done ! Warning message:
Output directory does not exist ! Creating it !
1 Fastq files are going to be processed !
Mapping mysample_S1_L004_R2_extracted.fastq file
STAR --runThreadN 16 --genomeDir /Viral_Track/mouse/index --readFilesIn Viral_Track/ mouse/mysample_S1_L004_R2_extracted.fastq --outSAMattributes NH HI AS nM NM XS --outFileNamePrefix /Viral_Track/mouse/ouput/mysample_S1_L004_R2_extracted/mysample_S1_L004_R2extracted --outS AMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMatchNmin 35 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6
STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Jul 18 15:24:34 ..... started STAR run
Jul 18 15:24:34 ..... loading genome
Jul 18 15:24:58 ..... started 1st pass mapping
Jul 18 16:53:02 ..... finished 1st pass mapping
Jul 18 16:53:03 ..... inserting junctions into the genome indices
Jul 18 16:56:33 ..... started mapping
Jul 18 19:22:57 ..... finished mapping
Jul 18 19:22:58 ..... started sorting BAM
Jul 18 19:54:04 ..... finished successfully
Mapping ofmysample_S1_L004_R2_extracted.fastq done !
All fastq files have been mapped successfully
Starting the BAM file analysis
Indexing of the bam file for mysample_S1_L004_R2_extracted is done
Computing stat file for the bam file for mysample_S1_L004_R2_extracted is done
Checking the mapping quality of each virus...
[main_samview] region "NA" specifies an unknown reference name. Continue anyway.
[main_samview] region "NA.1" specifies an unknown reference name. Continue anyway.
Export of the viral SAM file done for mysample_S1_L004_R2_extracted
Error in { :
task 1 failed - "In range 1: at least two out of 'start', 'end', and 'width', must
be supplied."
Calls: %dopar% ->
Execution halted
Do you know what happens? I try different ways but can't solve this problem.
Thanks a lot
Lee
Hi, Thank you so much for the nice software. When I run the Viral_Track_scanning.R a error were present as follows;
Loading of the libraries.... ... done ! Warning message: Output directory does not exist ! Creating it ! 1 Fastq files are going to be processed ! Mapping mysample_S1_L004_R2_extracted.fastq file STAR --runThreadN 16 --genomeDir /Viral_Track/mouse/index --readFilesIn Viral_Track/ mouse/mysample_S1_L004_R2_extracted.fastq --outSAMattributes NH HI AS nM NM XS --outFileNamePrefix /Viral_Track/mouse/ouput/mysample_S1_L004_R2_extracted/mysample_S1_L004_R2extracted --outS AMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMatchNmin 35 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6 STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jul 18 15:24:34 ..... started STAR run Jul 18 15:24:34 ..... loading genome Jul 18 15:24:58 ..... started 1st pass mapping Jul 18 16:53:02 ..... finished 1st pass mapping Jul 18 16:53:03 ..... inserting junctions into the genome indices Jul 18 16:56:33 ..... started mapping Jul 18 19:22:57 ..... finished mapping Jul 18 19:22:58 ..... started sorting BAM Jul 18 19:54:04 ..... finished successfully Mapping ofmysample_S1_L004_R2_extracted.fastq done ! All fastq files have been mapped successfully Starting the BAM file analysis Indexing of the bam file for mysample_S1_L004_R2_extracted is done Computing stat file for the bam file for mysample_S1_L004_R2_extracted is done Checking the mapping quality of each virus... [main_samview] region "NA" specifies an unknown reference name. Continue anyway. [main_samview] region "NA.1" specifies an unknown reference name. Continue anyway. Export of the viral SAM file done for mysample_S1_L004_R2_extracted Error in { : task 1 failed - "In range 1: at least two out of 'start', 'end', and 'width', must be supplied." Calls: %dopar% ->
Execution halted
Do you know what happens? I try different ways but can't solve this problem. Thanks a lot Lee