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Starting on       : Sat Aug  8 23:03:53 EDT 2020
Running on node   : scc-kb5
Current job ID    : 8687825
Current job name  : mm10_ensembl_GeneBody_NRCombined
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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Aug 08 23:09:08 ..... Started STAR run
Aug 08 23:09:08 ... Starting to generate Genome files
Aug 08 23:11:15 ... starting to sort  Suffix Array. This may take a long time...
Aug 08 23:11:30 ... sorting Suffix Array chunks and saving them to disk...
Aug 09 01:16:50 ... loading chunks from disk, packing SA...
Aug 09 01:17:35 ... Finished generating suffix array
Aug 09 01:17:35 ... Generating Suffix Array index
Aug 09 01:21:22 ... Completed Suffix Array index
Aug 09 01:21:22 ..... Processing annotations GTF
Aug 09 01:21:26 ... writing Genome to disk ...
Aug 09 01:43:50 ... writing Suffix Array to disk ...
Aug 09 02:43:40 ... writing SAindex to disk
Aug 09 02:55:56 ..... Finished successfully
Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/mm10_ensembl_GeneBody_NRCombined
...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/mm10_ensembl_GeneBody_NRCombined ...
Finished  .............. Sun Aug  9 02:55:58 EDT 2020