==========================================================
Starting on       : Mon Aug  3 16:41:35 EDT 2020
Running on node   : scc-tl1
Current job ID    : 8514443
Current job name  : mm10_ensembl_TRANS
Task index number : 
==========================================================
/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.
-------------------------------------------------------------------------------

Aug 03 16:48:46 ..... Started STAR run
Aug 03 16:48:46 ... Starting to generate Genome files
Aug 03 16:50:10 ... starting to sort  Suffix Array. This may take a long time...
Aug 03 16:50:17 ... sorting Suffix Array chunks and saving them to disk...
Aug 03 17:25:07 ... loading chunks from disk, packing SA...
Aug 03 17:25:35 ... Finished generating suffix array
Aug 03 17:25:35 ... Generating Suffix Array index
Aug 03 17:27:47 ... Completed Suffix Array index
Aug 03 17:27:47 ..... Processing annotations GTF
Aug 03 17:27:54 ... writing Genome to disk ...
Aug 03 17:28:42 ... writing Suffix Array to disk ...
Aug 03 17:29:56 ... writing SAindex to disk
Aug 03 17:30:17 ..... Finished successfully
Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/mm10_premrna_PCG-newlncs_TRANS
...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_premrna_PCG-newlncs_TRANS ...
Finished  .............. Mon Aug  3 17:30:18 EDT 2020