----------------------- Need shift 1 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- Sample_ID: G168_G169_M12 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files MODE: intersection-nonempty STRANDEDNESS_HTSeq: reverse FEATURE_ID: gene_id SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08a_Extract_Counts_HTSeq ANNOTATION_FILE: Intron_Only_Regions.gtf FEATURE_TYPE: Intronic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 15 21:43:09 EDT 2019 Running on node : scc-yd4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08a_Extract_Counts_HTSeq Current job ID : 5226007 Current job name : Step_08a_G168_G169_M12 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5226007.1.y Loading required modules... List files in scratch directory: total 1.8G drwx------ 2 kkarri waxmanlab 4.0K Apr 15 21:58 . drwxrwxrwt. 24 root root 4.0K Apr 15 21:53 .. -rw-r--r-- 1 kkarri waxmanlab 0 Apr 15 21:58 G168_G169_M12_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 1.8G Apr 15 21:58 G168_G169_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 18M Apr 15 21:58 Intron_Only_Regions.gtf Starting to run my commands Starting samtools and htseq-count Starting splice read filter Ending splice read filter samtools view G168_G169_M12'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf > G168_G169_M12_HTSeq.out Ending samtools and htseq-count List files in scratch total 36G drwx------ 2 kkarri waxmanlab 4.0K Apr 15 22:23 . drwxrwxrwt. 24 root root 4.0K Apr 15 22:13 .. -rw-r--r-- 1 kkarri waxmanlab 233K Apr 15 22:23 G168_G169_M12_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 925M Apr 15 22:05 G168_G169_M12_primary_no_splice.bam -rw-r--r-- 1 kkarri waxmanlab 1.8G Apr 15 21:58 G168_G169_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 1.7G Apr 15 22:13 G168_G169_M12_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 98 Apr 15 22:23 HTSeq_Extra_Lines.txt -rw-r--r-- 1 kkarri waxmanlab 892 Apr 15 22:00 Header.txt -rw-r--r-- 1 kkarri waxmanlab 18M Apr 15 21:58 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri waxmanlab 38K Apr 15 22:23 RefSeq_Genes_Zero_Count.txt -rw-r--r-- 1 kkarri waxmanlab 16G Apr 15 22:02 temp1.sam -rw-r--r-- 1 kkarri waxmanlab 7.8G Apr 15 22:02 temp2.sam -rw-r--r-- 1 kkarri waxmanlab 7.8G Apr 15 22:02 temp3.sam ========================================================== Finished on : Mon Apr 15 22:23:09 EDT 2019 0 hours, 40 minutes and 0 seconds elapsed. ==========================================================