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Starting on       : Mon Jun 14 16:06:32 EDT 2021
Running on node   : scc-tl4
Current job ID    : 6981467
Current job name  : IntronicRef_for_TCPOAnalysis
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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Jun 14 16:09:57 ..... Started STAR run
Jun 14 16:09:57 ... Starting to generate Genome files
Jun 14 16:11:18 ... starting to sort  Suffix Array. This may take a long time...
Jun 14 16:11:25 ... sorting Suffix Array chunks and saving them to disk...
Jun 14 16:47:42 ... loading chunks from disk, packing SA...
Jun 14 16:48:11 ... Finished generating suffix array
Jun 14 16:48:11 ... Generating Suffix Array index
Jun 14 16:50:25 ... Completed Suffix Array index
Jun 14 16:50:25 ..... Processing annotations GTF
Jun 14 16:50:29 ..... Inserting junctions into the genome indices
Jun 14 16:56:32 ... writing Genome to disk ...
Jun 14 16:57:00 ... writing Suffix Array to disk ...
Jun 14 16:58:15 ... writing SAindex to disk
Jun 14 16:58:34 ..... Finished successfully
Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/IntronicRef_for_TCPOAnalysis
...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/IntronicRef_for_TCPOAnalysis ...
Finished  .............. Mon Jun 14 16:58:35 EDT 2021