========================================================== Starting on : Wed Jul 6 11:04:11 EDT 2022 Running on node : scc-ph3 Current job ID : 5686344 Current job name : mm10-ARC-ModifiedIntronic-Formatted10xRef Task index number : ========================================================== Jul 06 11:06:11 ..... started STAR run Jul 06 11:06:11 ... starting to generate Genome files Jul 06 11:07:39 ... starting to sort Suffix Array. This may take a long time... Jul 06 11:07:45 ... sorting Suffix Array chunks and saving them to disk... Jul 06 11:38:58 ... loading chunks from disk, packing SA... Jul 06 11:39:23 ... finished generating suffix array Jul 06 11:39:23 ... generating Suffix Array index Jul 06 11:41:12 ... completed Suffix Array index Jul 06 11:41:12 ..... processing annotations GTF Jul 06 11:41:20 ..... inserting junctions into the genome indices Jul 06 11:46:29 ... writing Genome to disk ... Jul 06 11:46:58 ... writing Suffix Array to disk ... Jul 06 11:48:16 ... writing SAindex to disk Jul 06 11:48:33 ..... finished successfully >>> Creating reference for ModifiedIntronic_genes_scRNAseq_formatted_as10x <<< Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/snRNAseqRef/ModifiedIntronic_genes_scRNAseq_formatted_as10x ...done Writing genome FASTA file into reference folder... ...done Indexing genome FASTA file... ...done Writing genes GTF file into reference folder... ...done Generating STAR genome index (may take over 8 core hours for a 3Gb genome)... ...done. Writing genome metadata JSON file into reference folder... Computing hash of genome FASTA file... ...done Computing hash of genes GTF file... ...done ...done Generating bwa index (may take over an hour for a 3Gb genome)... [bwa_index] Pack FASTA... 20.44 sec [bwa_index] Construct BWT for the packed sequence... 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[BWTIncConstructFromPacked] 600 iterations done. 5431568732 characters processed. [BWTIncConstructFromPacked] 610 iterations done. 5454099340 characters processed. [bwt_gen] Finished constructing BWT in 614 iterations. [bwa_index] 1899.04 seconds elapse. [bwa_index] Update BWT... 13.89 sec [bwa_index] Pack forward-only FASTA... 13.47 sec [bwa_index] Construct SA from BWT and Occ... 647.60 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/snRNAseqRef/ModifiedIntronic_genes_scRNAseq_formatted_as10x/fasta/genome.fa [main] Real time: 2669.995 sec; CPU: 2594.444 sec done Writing TSS and transcripts bed file... ...done Writing genome metadata JSON file into reference folder... Computing hash of genome FASTA file... ...done Computing hash of genes GTF file... ...done ...done >>> Reference successfully created at ModifiedIntronic_genes_scRNAseq_formatted_as10x <<< Finished .............. Wed Jul 6 12:33:37 EDT 2022