----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: WT11 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 05:08:35 EDT 2019 Running on node : scc-ka6 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5782360 Current job name : Step_08a_WT11 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5782360.1.linga Loading required modules... List files in scratch directory: total 335M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:15 . drwxrwxrwt. 68 root root 92K Apr 30 05:14 .. -rw-r--r-- 1 kkarri waxmanlab 72M Apr 30 05:09 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 30 05:15 WT11_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 264M Apr 30 05:09 WT11_primary_unique.bam Starting to run my commands Starting samtools and htseq-count samtools view WT11'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf > WT11_HTSeq.out Ending samtools and htseq-count List files in scratch total 745M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:20 . drwxrwxrwt. 58 root root 92K Apr 30 05:37 .. -rw-r--r-- 1 kkarri waxmanlab 72M Apr 30 05:09 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 235K Apr 30 05:39 WT11_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 264M Apr 30 05:09 WT11_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 410M Apr 30 05:20 WT11_sorted.bam ========================================================== Finished on : Tue Apr 30 05:39:41 EDT 2019 0 hours, 31 minutes and 8 seconds elapsed. ==========================================================