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Starting on       : Thu Sep 19 10:06:14 EDT 2019
Running on node   : scc-kb4
Current job ID    : 9439002
Current job name  : mm10_pcg-only_usethis
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 19 10:11:05 ..... Started STAR run
Sep 19 10:11:05 ... Starting to generate Genome files
Sep 19 10:13:17 ... starting to sort  Suffix Array. This may take a long time...
Sep 19 10:13:33 ... sorting Suffix Array chunks and saving them to disk...
Sep 19 11:20:48 ... loading chunks from disk, packing SA...
Sep 19 11:21:30 ... Finished generating suffix array
Sep 19 11:21:30 ... Generating Suffix Array index
Sep 19 11:24:42 ... Completed Suffix Array index
Sep 19 11:24:42 ..... Processing annotations GTF
Sep 19 11:24:43 ... writing Genome to disk ...
Sep 19 11:25:12 ... writing Suffix Array to disk ...
Sep 19 11:26:29 ... writing SAindex to disk
Sep 19 11:26:48 ..... Finished successfully
Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_v1.0_pcg-only
...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/mm10_premrna_v1.0_pcg-only ...
Finished  .............. Thu Sep 19 11:26:50 EDT 2019