----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: G166_M9 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/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/G166_PCA_ENV/Scripts/08a_Extract_Counts_HTSeq ANNOTATION_FILE: Intron_Only_Regions.gtf FEATURE_TYPE: Intronic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 23 05:01:50 EDT 2019 Running on node : scc-kb8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5533328 Current job name : Step_08a_G166_M9 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5533328.1.linga Loading required modules... List files in scratch directory: total 666M drwx------ 2 kkarri waxmanlab 4.0K Apr 23 05:02 . drwxrwxrwt. 21 root root 112K Apr 23 05:02 .. -rw-r--r-- 1 kkarri waxmanlab 0 Apr 23 05:02 G166_M9_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 649M Apr 23 05:01 G166_M9_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 18M Apr 23 05:02 Intron_Only_Regions.gtf Starting to run my commands Starting samtools and htseq-count Starting splice read filter Ending splice read filter samtools view G166_M9'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf > G166_M9_HTSeq.out Ending samtools and htseq-count List files in scratch total 21G drwx------ 2 kkarri waxmanlab 4.0K Apr 23 06:03 . drwxrwxrwt. 18 root root 112K Apr 23 06:03 .. -rw-r--r-- 1 kkarri waxmanlab 239K Apr 23 06:03 G166_M9_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 632M Apr 23 05:10 G166_M9_primary_no_splice.bam -rw-r--r-- 1 kkarri waxmanlab 649M Apr 23 05:01 G166_M9_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 1.1G Apr 23 05:20 G166_M9_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 99 Apr 23 06:03 HTSeq_Extra_Lines.txt -rw-r--r-- 1 kkarri waxmanlab 879 Apr 23 05:03 Header.txt -rw-r--r-- 1 kkarri waxmanlab 18M Apr 23 05:02 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri waxmanlab 38K Apr 23 06:03 RefSeq_Genes_Zero_Count.txt -rw-r--r-- 1 kkarri waxmanlab 6.1G Apr 23 05:05 temp1.sam -rw-r--r-- 1 kkarri waxmanlab 6.0G Apr 23 05:05 temp2.sam -rw-r--r-- 1 kkarri waxmanlab 6.0G Apr 23 05:05 temp3.sam ========================================================== Finished on : Tue Apr 23 06:03:50 EDT 2019 1 hours, 2 minutes and 0 seconds elapsed. ==========================================================