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Starting on       : Wed Sep 18 12:30:14 EDT 2019
Running on node   : scc-wk1
Current job ID    : 9423894
Current job name  : mm10_10X_G171B_ERCC_omp28
Task index number : 
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/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/bin
cellranger count (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
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Martian Runtime - '3.1.0-v3.2.3'
Serving UI at http://scc-wk1:38602?auth=OwaRySiEfP2fNEbbDJQuB568BLauQdcmSbKX_0nil0w

Running preflight checks (please wait)...
2019-09-18 12:30:16 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF
2019-09-18 12:30:17 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF.fork0.chnk0.main
2019-09-18 12:30:23 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF
Checking sample info...
Checking FASTQ folder...
Checking libraries...
Checking reference...
Checking reference_path (/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB) on scc-wk1...
Checking chemistry...
Checking optional arguments...
mrc: '3.1.0-v3.2.3'

mrp: '3.1.0-v3.2.3'

Anaconda: Python 2.7.14 :: Anaconda, Inc.

numpy: 1.14.2

scipy: 1.0.1

pysam: 0.14.1

h5py: 2.8.0

pandas: 0.22.0

STAR: STAR_2.5.1b

samtools: samtools 1.7
Using htslib 1.7
Copyright (C) 2018 Genome Research Ltd.

2019-09-18 12:30:31 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION
2019-09-18 12:30:32 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION.fork0.chnk0.main
2019-09-18 12:30:32 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES
2019-09-18 12:30:33 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES.fork0.chnk0.main
2019-09-18 12:30:33 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY
2019-09-18 12:30:34 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0.main
2019-09-18 12:30:35 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION
2019-09-18 12:30:36 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES
2019-09-18 12:30:39 [runtime] (progress)        ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Mapping reads...
2019-09-18 12:30:40 [runtime] (failed)          ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY

[error] Unable to detect the chemistry for the following dataset. Please validate it and/or specify the chemistry via the --chemistry argument.

Detect Report -- /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/H3LTJBBXX/10X_G171B_MissingLibrary_1_H3LTJBBXX (None):

R1 Total Reads:                    10000
R1 Sense Reads:                        0
R1 Antisense Reads:                   30
R2 Total Reads:                    10000
R2 Sense Reads:                        1
R2 Antisense Reads:                    1

There was not enough information to determine the nature of the library.

2019-09-18 12:30:40 Shutting down.
Waiting 6 seconds for UI to do final refresh.
Saving pipestance info to "10X_G171B_ERCC/10X_G171B_ERCC.mri.tgz"
For assistance, upload this file to 10x Genomics by running:

cellranger upload <your_email> "10X_G171B_ERCC/10X_G171B_ERCC.mri.tgz"

Finished  .............. Wed Sep 18 12:30:44 EDT 2019