----------------------- Start of variable list: ----------------------- Sample_ID: H12-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 23:45:06 EDT 2018 Running on node : scc-ka3 Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/04_TopHat_Paired_End Current job ID : 8792847 Current job name : Step_04_H12-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/8792847.1.linga Loading required modules... Here is the Left_List: SRR6576410_1.fastq.gz Here is the Right_List: SRR6576410_2.fastq.gz List files in the scratch directory: total 97M drwx------ 4 kkarri waxmanlab 4.0K Oct 12 23:45 . drwxrwxrwt. 74 root root 108K Oct 12 23:45 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Oct 12 23:45 Bowtie2Index -rw-r--r-- 1 kkarri waxmanlab 72M Oct 12 23:45 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 12M Oct 12 23:45 SRR6576410_1.fastq.gz -rw-r--r-- 1 kkarri waxmanlab 13M Oct 12 23:45 SRR6576410_2.fastq.gz drwxr-xr-x 2 kkarri waxmanlab 4.0K Oct 12 23:45 tophat2 Starting to run my commands Starting tophat tophat --no-coverage-search -o /scratch/8792847.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-unstranded -r -41 --mate-std-dev 150 Bowtie2Index/genome SRR6576410_1.fastq.gz SRR6576410_2.fastq.gz Ending tophat Starting samtools commands Ending samtools commands Starting spliced_read_counts Ending spliced_read_counts List files in scratch total 97M drwx------ 4 kkarri waxmanlab 4.0K Oct 13 00:12 . drwxrwxrwt. 70 root root 108K Oct 13 00:06 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Oct 12 23:45 Bowtie2Index -rw-r--r-- 1 kkarri waxmanlab 72M Oct 12 23:45 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 12M Oct 12 23:45 SRR6576410_1.fastq.gz -rw-r--r-- 1 kkarri waxmanlab 13M Oct 12 23:45 SRR6576410_2.fastq.gz -rw-r--r-- 1 kkarri waxmanlab 7 Oct 13 00:12 numunique_hits.txt drwxr-xr-x 3 kkarri waxmanlab 4.0K Oct 13 00:13 tophat2 ========================================================== Finished on : Sat Oct 13 00:13:07 EDT 2018 0 hours, 28 minutes and 1 seconds elapsed. ==========================================================