----------------------- Start of variable list: ----------------------- Sample_ID: N-3 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066 Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/Scripts/00_Setup_Pipeline Bowtie2Index_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/ GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf STRANDEDNESS: fr-secondstrand DISTANCE_BT_READ_PAIR: -86 ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Jun 24 17:29:25 EDT 2019 Running on node : scc-kb5 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/Scripts/04_TopHat_Paired_End Current job ID : 7056752 Current job name : Step_04_N-3 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/7056752.1.linga Loading required modules... Here is the Left_List: SRR7518412_1.fastq.gz Here is the Right_List: SRR7518412_2.fastq.gz List files in the scratch directory: total 3.7G drwx------ 3 varsha97 waxmanlab 4.0K Jun 24 17:34 . drwxrwxrwt. 15 root root 4.0K Jun 24 17:29 .. drwxr-xr-x 2 varsha97 waxmanlab 4.0K Jun 24 17:34 Bowtie2Index -rw-r--r-- 1 varsha97 waxmanlab 0 Jun 24 17:34 RefSeq_GeneBody.gtf -rw-r--r-- 1 varsha97 waxmanlab 1.8G Jun 24 17:30 SRR7518412_1.fastq.gz -rw-r--r-- 1 varsha97 waxmanlab 2.0G Jun 24 17:31 SRR7518412_2.fastq.gz Starting to run my commands Starting tophat tophat --no-coverage-search -o /scratch/7056752.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-secondstrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR7518412_1.fastq.gz SRR7518412_2.fastq.gz Ending tophat Starting samtools commands Ending samtools commands Starting spliced_read_counts Ending spliced_read_counts List files in scratch total 282K dr-xr-xr-x. 35 root root 4.0K Jun 11 22:58 . dr-xr-xr-x. 35 root root 4.0K Jun 11 22:58 .. drwxr----- 3 root root 4.0K Jun 9 03:21 .pki -rw-r--r-- 1 root root 78K Jun 11 22:58 .readahead drwxr-xr-x. 3 root root 4.0K Jun 8 17:08 ad drwxr-xr-x. 2 root root 4.0K Jun 8 17:08 archive drwxr-xr-x. 3 root root 4.0K Jun 8 17:08 auto lrwxrwxrwx. 1 root root 7 Jun 8 16:33 bin -> usr/bin dr-xr-xr-x. 6 root root 4.0K Jun 8 17:13 boot drwxr-xr-x. 2 root root 4.0K Jun 8 17:02 cms drwxr-xr-x 20 root root 3.6K Jun 21 14:41 dev drwxr-xr-x. 155 root root 12K Jun 17 12:09 etc drwxr-xr-x. 3 root root 4.0K Apr 11 2018 home drwxr-xr-x 2 root root 0 Jun 11 22:58 hosts drwxr-xr-x 2 root root 0 Jun 11 22:58 krb5net lrwxrwxrwx. 1 root root 7 Jun 8 16:33 lib -> usr/lib lrwxrwxrwx. 1 root root 9 Jun 8 16:33 lib64 -> usr/lib64 drwx------. 2 root root 16K Jun 8 16:30 lost+found drwxr-xr-x. 2 root root 4.0K Apr 11 2018 media drwxr-xr-x. 2 root root 4.0K Apr 11 2018 mnt drwxr-xr-x 3 root root 0 Jun 24 17:29 net drwxr-xr-x. 6 root root 4.0K Jun 8 17:08 opt dr-xr-xr-x 687 root root 0 Jun 11 22:57 proc drwxr-xr-x 517 root root 32K Jun 24 17:19 project drwxr-xr-x 559 root root 32K Jun 24 17:19 projectnb lrwxrwxrwx. 1 root root 16 Jun 8 17:08 protected -> /share/protected drwxr-xr-x. 5 root root 4.0K Jun 8 17:08 restricted drwxr-x---. 3 root root 4.0K Jun 8 18:47 root lrwxrwxrwx. 1 root root 19 Jun 8 17:08 rproject -> /restricted/project lrwxrwxrwx. 1 root root 21 Jun 8 17:08 rprojectnb -> /restricted/projectnb drwxr-xr-x 35 root root 1.2K Jun 23 10:19 run lrwxrwxrwx. 1 root root 8 Jun 8 16:33 sbin -> usr/sbin drwxrwxrwt. 15 root root 4.0K Jun 24 17:29 scratch drwxr-xr-x 11 root root 512 Jun 13 2018 share drwxr-xr-x. 2 root root 4.0K Apr 11 2018 srv dr-xr-xr-x 13 root root 0 Jun 18 11:06 sys drwxrwxrwt. 11 root root 4.0K Jun 24 17:30 tmp lrwxrwxrwx. 1 root root 18 Jun 8 17:08 unprotected -> /share/unprotected drwxr-xr-x. 14 root root 4.0K Jun 8 17:02 usr drwxr-xr-x 4 root root 512 Aug 8 2016 usr1 drwxr-xr-x 5 root root 512 Mar 11 2017 usr2 drwxr-xr-x 4 root root 512 Jul 31 2014 usr3 drwxr-xr-x 39 root root 32K Mar 7 17:17 usr4 drwxr-xr-x. 24 root root 4.0K Jun 8 17:13 var ========================================================== Finished on : Mon Jun 24 17:34:58 EDT 2019 0 hours, 5 minutes and 33 seconds elapsed. ==========================================================