----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: KI2 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 05:08:51 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 : 5782382 Current job name : Step_08a_KI2 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5782382.1.linga Loading required modules... List files in scratch directory: total 304M drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:20 . drwxrwxrwt. 72 root root 84K Apr 30 05:20 .. -rw-r--r-- 1 kkarri waxmanlab 18M Apr 30 05:14 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 30 05:20 KI2_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 287M Apr 30 05:14 KI2_primary_unique.bam Starting to run my commands Starting samtools and htseq-count Starting splice read filter Ending splice read filter samtools view KI2'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf > KI2_HTSeq.out Ending samtools and htseq-count List files in scratch total 6.1G drwx------ 2 kkarri waxmanlab 4.0K Apr 30 05:50 . drwxrwxrwt. 57 root root 84K Apr 30 05:44 .. -rw-r--r-- 1 kkarri waxmanlab 97 Apr 30 05:50 HTSeq_Extra_Lines.txt -rw-r--r-- 1 kkarri waxmanlab 883 Apr 30 05:24 Header.txt -rw-r--r-- 1 kkarri waxmanlab 18M Apr 30 05:14 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 226K Apr 30 05:50 KI2_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 240M Apr 30 05:28 KI2_primary_no_splice.bam -rw-r--r-- 1 kkarri waxmanlab 287M Apr 30 05:14 KI2_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 369M Apr 30 05:33 KI2_sorted.bam -rwxr-xr-x 1 kkarri waxmanlab 38K Apr 30 05:50 RefSeq_Genes_Zero_Count.txt -rw-r--r-- 1 kkarri waxmanlab 2.0G Apr 30 05:25 temp1.sam -rw-r--r-- 1 kkarri waxmanlab 1.6G Apr 30 05:26 temp2.sam -rw-r--r-- 1 kkarri waxmanlab 1.6G Apr 30 05:26 temp3.sam ========================================================== Finished on : Tue Apr 30 05:50:50 EDT 2019 0 hours, 41 minutes and 59 seconds elapsed. ==========================================================