----------------------- 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: Intron_Only_Regions.gtf FEATURE_TYPE: Intronic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 30 05:12:41 EDT 2019 Running on node : scc-kb5 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5782389 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/5782389.1.linga Loading required modules... List files in scratch directory: total 307M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:28 . drwxrwxrwt. 57 root root 268K Apr 30 05:20 .. -rw-r--r-- 1 kkarri waxmanlab 18M Apr 30 05:20 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 30 05:28 KI3_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 290M Apr 30 05:20 KI3_primary_unique.bam Starting to run my commands Starting samtools and htseq-count Starting splice read filter Ending splice read filter samtools view KI3'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf > KI3_HTSeq.out Ending samtools and htseq-count List files in scratch total 6.1G drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:48 . drwxrwxrwt. 45 root root 268K Apr 30 05:46 .. -rw-r--r-- 1 kkarri waxmanlab 97 Apr 30 05:48 HTSeq_Extra_Lines.txt -rw-r--r-- 1 kkarri waxmanlab 881 Apr 30 05:30 Header.txt -rw-r--r-- 1 kkarri waxmanlab 18M Apr 30 05:20 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 226K Apr 30 05:48 KI3_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 242M Apr 30 05:32 KI3_primary_no_splice.bam -rw-r--r-- 1 kkarri waxmanlab 290M Apr 30 05:20 KI3_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 372M Apr 30 05:36 KI3_sorted.bam -rwxr-xr-x 1 kkarri waxmanlab 38K Apr 30 05:48 RefSeq_Genes_Zero_Count.txt -rw-r--r-- 1 kkarri waxmanlab 2.0G Apr 30 05:30 temp1.sam -rw-r--r-- 1 kkarri waxmanlab 1.7G Apr 30 05:31 temp2.sam -rw-r--r-- 1 kkarri waxmanlab 1.7G Apr 30 05:31 temp3.sam ========================================================== Finished on : Tue Apr 30 05:48:02 EDT 2019 0 hours, 35 minutes and 21 seconds elapsed. ==========================================================