----------------------- 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: RefSeq_GeneBody.gtf FEATURE_TYPE: exon ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 30 05:08:39 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 : 5782391 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/5782391.1.linga Loading required modules... List files in scratch directory: total 361M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:17 . drwxrwxrwt. 66 root root 92K Apr 30 05:16 .. -rw-r--r-- 1 kkarri waxmanlab 0 Apr 30 05:17 KI3_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 290M Apr 30 05:14 KI3_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 72M Apr 30 05:14 RefSeq_GeneBody.gtf Starting to run my commands Starting samtools and htseq-count samtools view KI3'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf > KI3_HTSeq.out Ending samtools and htseq-count List files in scratch total 815M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:22 . drwxrwxrwt. 56 root root 92K Apr 30 05:41 .. -rw-r--r-- 1 kkarri waxmanlab 236K Apr 30 05:42 KI3_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 290M Apr 30 05:14 KI3_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 454M Apr 30 05:22 KI3_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 72M Apr 30 05:14 RefSeq_GeneBody.gtf ========================================================== Finished on : Tue Apr 30 05:42:01 EDT 2019 0 hours, 33 minutes and 23 seconds elapsed. ==========================================================