----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: WT5 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files MODE: intersection-nonempty STRANDEDNESS_HTSeq: reverse FEATURE_ID: gene_id SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq ANNOTATION_FILE: Exon_Only_Regions.gtf FEATURE_TYPE: Exonic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 30 05:29:42 EDT 2019 Running on node : scc-kb2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5782307 Current job name : Step_08a_WT5 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5782307.1.linga Loading required modules... List files in scratch directory: total 311M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:41 . drwxrwxrwt. 83 root root 92K Apr 30 05:33 .. -rw-r--r-- 1 kkarri waxmanlab 19M Apr 30 05:36 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Apr 30 05:36 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 30 05:41 WT5_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 276M Apr 30 05:36 WT5_primary_unique.bam Starting to run my commands Starting samtools and htseq-count Starting Intron_Only_Regions read overlap filter Ending Intron_Only_Regions read overlap filter samtools view WT5'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf > WT5_HTSeq.out Ending samtools and htseq-count List files in scratch total 849M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:47 . drwxrwxrwt. 79 root root 92K Apr 30 05:59 .. -rw-r--r-- 1 kkarri waxmanlab 19M Apr 30 05:36 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Apr 30 05:36 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 235K Apr 30 05:59 WT5_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 208M Apr 30 05:44 WT5_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 276M Apr 30 05:36 WT5_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 331M Apr 30 05:47 WT5_sorted.bam ========================================================== Finished on : Tue Apr 30 05:59:59 EDT 2019 0 hours, 30 minutes and 17 seconds elapsed. ==========================================================