----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: WT8 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: RefSeq_GeneBody.gtf FEATURE_TYPE: exon ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 30 05:08:47 EDT 2019 Running on node : scc-kb6 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5782336 Current job name : Step_08a_WT8 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5782336.1.linga Loading required modules... List files in scratch directory: total 354M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:18 . drwxrwxrwt. 73 root root 84K Apr 30 05:19 .. -rw-r--r-- 1 kkarri waxmanlab 72M Apr 30 05:13 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 30 05:18 WT8_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 283M Apr 30 05:13 WT8_primary_unique.bam Starting to run my commands Starting samtools and htseq-count samtools view WT8'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf > WT8_HTSeq.out Ending samtools and htseq-count List files in scratch total 799M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:28 . drwxrwxrwt. 54 root root 84K Apr 30 05:52 .. -rw-r--r-- 1 kkarri waxmanlab 72M Apr 30 05:13 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 236K Apr 30 05:55 WT8_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 283M Apr 30 05:13 WT8_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 445M Apr 30 05:28 WT8_sorted.bam ========================================================== Finished on : Tue Apr 30 05:55:22 EDT 2019 0 hours, 46 minutes and 35 seconds elapsed. ==========================================================