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Starting on       : Fri Sep  6 15:04:14 EDT 2019
Running on node   : scc-ka4
Current job ID    : 9183587
Current job name  : mm9_test_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 06 15:10:09 ..... Started STAR run
Sep 06 15:10:09 ... Starting to generate Genome files
Sep 06 15:12:45 ... starting to sort  Suffix Array. This may take a long time...
Sep 06 15:13:02 ... sorting Suffix Array chunks and saving them to disk...
Sep 06 16:19:52 ... loading chunks from disk, packing SA...
Sep 06 16:20:44 ... Finished generating suffix array
Sep 06 16:20:44 ... Generating Suffix Array index
Sep 06 16:24:55 ... Completed Suffix Array index
Sep 06 16:24:55 ..... Processing annotations GTF
Sep 06 16:25:05 ..... Inserting junctions into the genome indices
Sep 06 16:37:15 ... writing Genome to disk ...
Sep 06 16:37:45 ... writing Suffix Array to disk ...
Sep 06 16:39:07 ... writing SAindex to disk
Sep 06 16:39:28 ..... Finished successfully
Creating new reference folder at /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/mm9_usethis
...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...
WARNING: The following transcripts appear on multiple chromosomes in the GTF:
NR_037313
NM_030742
NM_030741
NR_106201
NM_001193666
NR_029552
NM_001200055
NM_001270553
NR_106175
NR_110502
NR_028552
NR_110503
NM_011335
NM_001270457
NM_001099920
NM_001193668
NM_001167567
NM_177913
NM_145708
NR_002889
NM_001270431
NM_001025388
NM_001122668
NR_030454
NM_001270360
NM_001031622
NM_001270432
NM_001085530
NM_145601
NM_198667
NR_109835
NR_039557
NM_001167568
NM_016909
NR_044992
NM_018751
NM_145968
NM_011667
NM_001167793
NR_002445
NM_001102677
NM_001177580
NR_002883
NM_001297747
NR_035440
NM_001177471
NR_035409
NM_009362
NM_001025353
NM_001122734
NM_001012640
NR_033123
NM_023052
NR_002891
NM_001122678
NM_011022

This can indicate a problem with the reference or annotations. Only the first chromosome will be counted.
...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/mm9/mm9_usethis ...
Finished  .............. Fri Sep  6 16:39:30 EDT 2019