----------------------- Start of variable list: ----------------------- Sample_ID: F13-MAA000907-3_11_M-1-1 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline Bowtie2Index_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/Bowtie2 GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf STRANDEDNESS: fr-unstranded DISTANCE_BT_READ_PAIR: -41 ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Oct 12 23:09:09 EDT 2018 Running on node : scc-kb1 Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/04_TopHat_Paired_End Current job ID : 8792826 Current job name : Step_04_F13-MAA000907-3_11_M-1-1 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/8792826.1.linga Loading required modules... Here is the Left_List: SRR6576332_1.fastq.gz Here is the Right_List: SRR6576332_2.fastq.gz List files in the scratch directory: total 98M drwx------ 4 kkarri waxmanlab 4.0K Oct 12 23:09 . drwxrwxrwt. 82 root root 180K Oct 12 23:09 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Oct 12 23:09 Bowtie2Index -rw-r--r-- 1 kkarri waxmanlab 72M Oct 12 23:09 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 13M Oct 12 23:09 SRR6576332_1.fastq.gz -rw-r--r-- 1 kkarri waxmanlab 13M Oct 12 23:09 SRR6576332_2.fastq.gz drwxr-xr-x 2 kkarri waxmanlab 4.0K Oct 12 23:09 tophat2 Starting to run my commands Starting tophat tophat --no-coverage-search -o /scratch/8792826.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-unstranded -r -41 --mate-std-dev 150 Bowtie2Index/genome SRR6576332_1.fastq.gz SRR6576332_2.fastq.gz Ending tophat Starting samtools commands Ending samtools commands Starting spliced_read_counts Ending spliced_read_counts List files in scratch total 98M drwx------ 4 kkarri waxmanlab 4.0K Oct 12 23:36 . drwxrwxrwt. 80 root root 180K Oct 12 23:29 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Oct 12 23:09 Bowtie2Index -rw-r--r-- 1 kkarri waxmanlab 72M Oct 12 23:09 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 13M Oct 12 23:09 SRR6576332_1.fastq.gz -rw-r--r-- 1 kkarri waxmanlab 13M Oct 12 23:09 SRR6576332_2.fastq.gz -rw-r--r-- 1 kkarri waxmanlab 7 Oct 12 23:36 numunique_hits.txt drwxr-xr-x 3 kkarri waxmanlab 4.0K Oct 12 23:37 tophat2 ========================================================== Finished on : Fri Oct 12 23:37:18 EDT 2018 0 hours, 28 minutes and 9 seconds elapsed. ==========================================================