----------------------- 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: Exon_Only_Regions.gtf FEATURE_TYPE: Exonic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 23 05:01:12 EDT 2019 Running on node : scc-ka2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5533327 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/5533327.1.linga Loading required modules... List files in scratch directory: total 685M drwx------ 2 kkarri waxmanlab 4.0K Apr 23 05:02 . drwxrwxrwt. 72 root root 116K Apr 23 05:02 .. -rw-r--r-- 1 kkarri waxmanlab 19M Apr 23 05:02 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 23 05:02 G166_M9_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 649M Apr 23 05:02 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 Intron_Only_Regions read overlap filter Ending Intron_Only_Regions read overlap filter samtools view G166_M9'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf > G166_M9_HTSeq.out Ending samtools and htseq-count List files in scratch total 1.7G drwx------ 2 kkarri waxmanlab 4.0K Apr 23 05:14 . drwxrwxrwt. 68 root root 116K Apr 23 05:43 .. -rw-r--r-- 1 kkarri waxmanlab 19M Apr 23 05:02 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 235K Apr 23 05:45 G166_M9_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 382M Apr 23 05:07 G166_M9_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 649M Apr 23 05:02 G166_M9_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 666M Apr 23 05:14 G166_M9_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 18M Apr 23 05:02 Intron_Only_Regions.gtf ========================================================== Finished on : Tue Apr 23 05:45:26 EDT 2019 0 hours, 44 minutes and 14 seconds elapsed. ==========================================================