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Starting on       : Tue Sep 29 20:21:24 EDT 2020
Running on node   : scc-ph7
Current job ID    : 9838505
Current job name  : Final_mm10GTF_forscRNAseq
Task index number : 
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/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/bin
cellranger mkref (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
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Sep 29 20:24:56 ..... Started STAR run
Sep 29 20:24:56 ... Starting to generate Genome files
Sep 29 20:26:16 ... starting to sort  Suffix Array. This may take a long time...
Sep 29 20:26:23 ... sorting Suffix Array chunks and saving them to disk...
Sep 29 21:07:07 ... loading chunks from disk, packing SA...
Sep 29 21:07:33 ... Finished generating suffix array
Sep 29 21:07:33 ... Generating Suffix Array index
Sep 29 21:09:38 ... Completed Suffix Array index
Sep 29 21:09:38 ..... Processing annotations GTF
Sep 29 21:09:47 ..... Inserting junctions into the genome indices
Sep 29 21:16:20 ... writing Genome to disk ...
Sep 29 21:16:52 ... writing Suffix Array to disk ...
Sep 29 21:18:16 ... writing SAindex to disk
Sep 29 21:18:34 ..... Finished successfully
Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Final_mm10GTF_forscRNAseq
...done

Writing genome FASTA file into reference folder...
...done

Computing hash of genome FASTA file...
...done

Indexing genome FASTA file...
...done

Writing genes GTF file into reference folder...
...done

Computing hash of genes GTF file...
...done

Writing genes index file into reference folder (may take over 10 minutes for a 3Gb genome)...
...done

Writing genome metadata JSON file into reference folder...
...done

Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
...done.

>>> Reference successfully created! <<<

You can now specify this reference on the command line:
cellranger --transcriptome=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Final_mm10GTF_forscRNAseq ...
Finished  .............. Tue Sep 29 21:18:35 EDT 2020