Error running Viral_Track_cell_demultiplexing.R

[malonzm1]

Hi,

I run into the following error when running Viral_Track_cell_demultiplexing.R:

STAR --runThreadN 16 --genomeDir /scratch/cs/pan-autoimmune/utilities/viral-track/ --readFilesIn /scratch/cs/pan-autoimmune/data/umi-tools/scRNAseq/GSE137496/SRR10124077/SRR10124077_R2_extracted.fastq.gz --outSAMattributes NH HI AS nM NM XS --outFileNamePrefix /scratch/cs/pan-autoimmune/data/viral-track/scRNAseq/GSE137496/SRR10124077_R2_extracted/SRR10124077_R2extracted --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMatchNmin 35 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6 --readFilesCommand zcat STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Sep 13 12:30:17 ..... started STAR run Sep 13 12:30:17 ..... loading genome Sep 13 12:30:33 ..... started 1st pass mapping Sep 13 12:34:16 ..... finished 1st pass mapping Sep 13 12:34:16 ..... inserting junctions into the genome indices Sep 13 12:36:03 ..... started mapping Sep 13 12:39:41 ..... finished mapping Sep 13 12:39:44 ..... started sorting BAM Sep 13 12:40:34 ..... finished successfully Mapping ofSRR10124077_R2_extracted.fastq done ! All fastq files have been mapped successfully Starting the BAM file analysis Indexing of the bam file for SRR10124078_R2_extracted is done Computing stat file for the bam file for SRR10124078_R2_extracted is done Checking the mapping quality of each virus... Export of the viral SAM file done for SRR10124078_R2_extracted Exporting QC SRR10124078_R2_extracted ....4 viral sequences detected detected Exporting QC table for SRR10124078_R2_extracted .... done !Creating QC plot for SRR10124078_R2_extracted ....QC plot done ! Merging Viral SAM files identifiedViral detection step done !Indexing of the bam file for SRR10124077_R2_extracted is done Computing stat file for the bam file for SRR10124077_R2_extracted is done Checking the mapping quality of each virus... Export of the viral SAM file done for SRR10124077_R2_extracted Exporting QC SRR10124077_R2_extracted ....2 viral sequences detected detected Exporting QC table for SRR10124077_R2_extracted .... done !Creating QC plot for SRR10124077_R2_extracted ....QC plot done ! Merging Viral SAM files identifiedViral detection step done !Extracting viral alignments from the different plates ... done ! Merging the BAM files from different runs......done ! Performing StringTie transcriptome assembly... done ! Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Merging various GTF files... done ! 3 viral transcripts detected Transcript assembly step finished ! Error in normalizePath(files, mustWork = mustWork) : path[2]="/scratch/cs/pan-autoimmune/data/viral-track/scRNAseq/GSE137496/SRR10124077_R2_extracted///Reads_to_demultiplex.bam": No such file or directory Calls: suppressMessages ... featureCounts -> .check_and_NormPath -> normalizePath

I ran the same script with a test fastq file and it ran ok. Please advise.

Thanks and good day.