cellranger运行日志7

时间:2021-10-15 作者:qvyue

2.5h

root 06:58:34 /home/rstudio/data/rawx
$ cellranger count --id=XPBSh 
>  --transcriptome=/home/rstudio/opt/refdata-gex-GRCh38-2020-A 
>  --fastqs=/home/rstudio/data/rawx/xpbs 
>  --sample=XPBS 
>  --r1-length 26 
>  --r2-length 98
Martian Runtime - v4.0.4
Serving UI at http://BC-25-at-66-181.34-237:41199?auth=XD0Jha2cR5CkiEFQB2XwNg0BX21iWGKGQn7O4Lpo7zM

Running preflight checks (please wait)...
Checking sample info...
Checking FASTQ folder...
Checking reference...
Checking reference_path (/home/rstudio/opt/refdata-gex-GRCh38-2020-A) on BC-25-at-66-181.34-237...
Checking read 1 length...
Checking read 2 length...
Checking optional arguments...
mrc: v4.0.4

mrp: v4.0.4

Anaconda: Python 3.7.6

numpy: 1.19.2

scipy: 1.1.0

pysam: 0.16.0.1

h5py: 2.8.0

pandas: 0.24.2

STAR: 2.7.2a

samtools: samtools 1.10
Using htslib 1.10.2
Copyright (C) 2019 Genome Research Ltd.

2021-06-29 06:59:39 [runtime] (ready)           ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_BAMS
2021-06-29 06:59:39 [runtime] (run:local)       ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_BAMS.fork0.chnk0.main
2021-06-29 06:59:39 [runtime] (ready)           ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS
2021-06-29 06:59:39 [runtime] (ready)           ID.XPBSh.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX
2021-06-29 06:59:39 [runtime] (run:local)       ID.XPBSh.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX.fork0.chnk0.main
2021-06-29 06:59:39 [runtime] (ready)           ID.XPBSh.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX
2021-06-29 06:59:39 [runtime] (run:local)       ID.XPBSh.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main
2021-06-29 06:59:39 [runtime] (ready)           ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR._GEM_WELL_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY
2021-06-29 06:59:39 [runtime] (run:local)       ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR._GEM_WELL_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main
cellranger运行日志7
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cellranger运行日志7
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硬盘已用完。。。。

cellranger运行日志7
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删文件

cellranger运行日志7
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2021-06-29 09:29:46 [runtime] (run:local)       ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS.fork0.join
2021-06-29 09:29:46 [runtime] (join_complete)   ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS
2021-06-29 09:29:46 [runtime] (ready)           ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE
2021-06-29 09:29:46 [runtime] (run:local)       ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE.fork0.chnk0.main
2021-06-29 09:29:46 [runtime] (chunks_complete) ID.XPBSh.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE

Outputs:
- Run summary HTML:                         /home/rstudio/data/rawx/XPBSh/outs/web_summary.html
- Run summary CSV:                          /home/rstudio/data/rawx/XPBSh/outs/metrics_summary.csv
- BAM:                                      /home/rstudio/data/rawx/XPBSh/outs/possorted_genome_bam.bam
- BAM index:                                /home/rstudio/data/rawx/XPBSh/outs/possorted_genome_bam.bam.bai
- Filtered feature-barcode matrices MEX:    /home/rstudio/data/rawx/XPBSh/outs/filtered_feature_bc_matrix
- Filtered feature-barcode matrices HDF5:   /home/rstudio/data/rawx/XPBSh/outs/filtered_feature_bc_matrix.h5
- Unfiltered feature-barcode matrices MEX:  /home/rstudio/data/rawx/XPBSh/outs/raw_feature_bc_matrix
- Unfiltered feature-barcode matrices HDF5: /home/rstudio/data/rawx/XPBSh/outs/raw_feature_bc_matrix.h5
- Secondary analysis output CSV:            /home/rstudio/data/rawx/XPBSh/outs/analysis
- Per-molecule read information:            /home/rstudio/data/rawx/XPBSh/outs/molecule_info.h5
- CRISPR-specific analysis:                 null
- Loupe Browser file:                       /home/rstudio/data/rawx/XPBSh/outs/cloupe.cloupe
- Feature Reference:                        null
- Target Panel File:                        null

Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!

2021-06-29 09:29:52 Shutting down.
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