----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: KI3 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 05:28:12 EDT 2019 Running on node : scc-ka3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5782387 Current job name : Step_08a_KI3 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5782387.1.linga Loading required modules... List files in scratch directory: total 325M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:39 . drwxrwxrwt. 77 root root 108K Apr 30 05:28 .. -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 05:39 KI3_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 290M Apr 30 05:36 KI3_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 KI3'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf > KI3_HTSeq.out Ending samtools and htseq-count List files in scratch total 880M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:45 . drwxrwxrwt. 71 root root 108K Apr 30 05:56 .. -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 05:57 KI3_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 216M Apr 30 05:41 KI3_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 290M Apr 30 05:36 KI3_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 340M Apr 30 05:45 KI3_sorted.bam ========================================================== Finished on : Tue Apr 30 05:57:22 EDT 2019 0 hours, 29 minutes and 10 seconds elapsed. ==========================================================