GhobrialMoheb
commented
1 year ago @PierreBSC , I have got a new error message:
Aug 04 15:44:28 ..... started STAR run
Aug 04 15:44:28 ..... loading genome
Aug 04 15:45:37 ..... started 1st pass mapping
Aug 04 15:46:02 ..... finished 1st pass mapping
Aug 04 15:46:02 ..... inserting junctions into the genome indices
Aug 04 15:47:38 ..... started mapping
Aug 04 15:48:05 ..... finished mapping
Aug 04 15:48:09 ..... started sorting BAM
Aug 04 15:48:17 ..... finished successfully
Mapping ofhgmm_100_R2_extracted.fastq done !
All fastq files have been mapped successfully
Starting the BAM file analysis
Indexing of the bam file for hgmm_100_R2_extracted is done
Computing stat file for the bam file for hgmm_100_R2_extracted is done
Checking the mapping quality of each virus...
Export of the viral SAM file done for hgmm_100_R2_extracted
Error in colnames<-(*tmp*, value = c("N_reads", "N_unique_reads", :
attempt to set 'colnames' on an object with less than two dimensions
Calls: colnames<- -> colnames<-
Execution halted
I am getting this error (highlighted in bold:
Loading of the libraries.... Warning message: multiple methods tables found for ‘rowRanges’ ... done ! [[1]]
Warning message: In read.table(Parameter_target_files, header = F, sep = "\t") : incomplete final line found by readTableHeader on '/mnt/c/Users/mohebg/Desktop/Viral_Track/Target_file.txt' 1 Fastq files are going to be processed ! Mapping hgmm_100_R2_extracted.fastq file STAR --runThreadN 20 --genomeDir /mnt/c/Users/mohebg/Desktop/newscanpyinR/index/ --readFilesIn /mnt/c/Users/mohebg/Desktop/newscanpyinR/hgmm_100_R2_extracted.fastq --outSAMattributes NH HI AS nM NM XS --outFileNamePrefix /mnt/c/Users/mohebg/Desktop//Viral_Track/Test_COVID//hgmm_100_R2_extracted/hgmm_100_R2extracted --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMatchNmin 35 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Aug 03 18:28:11 ..... started STAR run Aug 03 18:28:11 ..... loading genome Aug 03 18:29:40 ..... started 1st pass mapping Aug 03 18:30:06 ..... finished 1st pass mapping Aug 03 18:30:06 ..... inserting junctions into the genome indices Aug 03 18:31:58 ..... started mapping Aug 03 18:32:26 ..... finished mapping Aug 03 18:32:31 ..... started sorting BAM Aug 03 18:32:40 ..... finished successfully Mapping ofhgmm_100_R2_extracted.fastq done ! Warning message: In dir.create(temp_output_dir) : '/mnt/c/Users/mohebg/Desktop//Viral_Track/Test_COVID//hgmm_100_R2_extracted' already exists All fastq files have been mapped successfully Starting the BAM file analysis Indexing of the bam file for hgmm_100_R2_extracted is done Computing stat file for the bam file for hgmm_100_R2_extracted is done Checking the mapping quality of each virus... Export of the viral SAM file done for hgmm_100_R2_extracted Error in { : task 1 failed - "different row counts implied by arguments" Calls: %dopar% ->