evolvedmicrobe
commented
3 years ago Cell Ranger can't be used with data that wasn't produced on 10X machines, so this is expected behavior.
Closed leeyoyohku closed 3 years ago
evolvedmicrobe
commented
3 years ago Cell Ranger can't be used with data that wasn't produced on 10X machines, so this is expected behavior.
Dear Cellranger community,
I'm processing single cell RNAseq files from [this stem cell paper](Han X, Chen H, Huang D, Chen H et al. Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol 2018 Apr 5;19(1):47. PMID: 29622030), and want to compute RNA velocity after preprocess by cell ranger. I have downloaded using sra prefetch, covert to .fastq, and rename to "SRR6745454_S1_L001_R1_001.fastq" and "SRR6745454_S1_L001_R2_001.fastq". Then when I run
cellranger count -s SRR6745454 --transcriptome /home/yoyolab/reference/refdata-gex-GRCh38-2020-A --id sc1 --fastqs ../0_fastq_dump, I got the following messages:`Martian Runtime - v4.0.0 Serving UI at http://liulab:44617?auth=d8vgosKrYvPe6ihi1-OhAHA5qce3F37_mRCqxEESfn0
Running preflight checks (please wait)... Checking sample info... Checking FASTQ folder... Checking reference... Checking reference_path (/home/yoyolab/reference/refdata-gex-GRCh38-2020-A) on liulab... Checking chemistry... Checking optional arguments... mrc: v4.0.0
mrp: v4.0.0
Anaconda: Python 2.7.15 :: 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.
2020-11-15 15:46:56 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.EMPTY_IF_NULL 2020-11-15 15:46:56 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.EMPTY_IF_NULL.fork0.chnk0.main 2020-11-15 15:46:56 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.MAKE_BASIC_CONFIG 2020-11-15 15:46:56 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.MAKE_BASIC_CONFIG.fork0.chnk0.main 2020-11-15 15:46:56 [runtime] (chunks_complete) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.MAKE_BASIC_CONFIG 2020-11-15 15:46:56 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.FULL_COUNT_INPUTS.EXPAND_SAMPLE_DEF 2020-11-15 15:46:56 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.FULL_COUNT_INPUTS.EXPAND_SAMPLE_DEF.fork0.chnk0.main 2020-11-15 15:46:57 [runtime] (chunks_complete) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.EMPTY_IF_NULL 2020-11-15 15:46:57 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_CHEMISTRY_DETECTOR.DETECT_CHEMISTRY 2020-11-15 15:46:57 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_CHEMISTRY_DETECTOR.DETECT_VDJ_RECEPTOR 2020-11-15 15:46:57 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS 2020-11-15 15:46:57 [runtime] (chunks_complete) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.FULL_COUNT_INPUTS.EXPAND_SAMPLE_DEF 2020-11-15 15:46:57 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.DETECT_COUNT_CHEMISTRY 2020-11-15 15:46:57 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2020-11-15 15:46:57 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG 2020-11-15 15:46:57 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG.fork0.chnk0.main 2020-11-15 15:46:58 [runtime] (chunks_complete) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES 2020-11-15 15:46:58 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES.fork0.chnk0.main 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES 2020-11-15 15:46:58 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES.fork0.chnk0.main 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION 2020-11-15 15:46:58 [runtime] (run:local) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION.fork0.chnk0.main 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_B_CLONOTYPE_ASSIGNER.GROUP_CLONOTYPES 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_B_CLONOTYPE_ASSIGNER.ASSEMBLE_CONSENSUS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_T_CLONOTYPE_ASSIGNER.GROUP_CLONOTYPES 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_REPORTER.VDJ_B_REPORTER.REPORT_CONTIGS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_T_CLONOTYPE_ASSIGNER.ASSEMBLE_CONSENSUS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_REPORTER.VDJ_B_REPORTER.SUMMARIZE_VDJ_REPORTS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_T_CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_REPORTER.VDJ_T_REPORTER.REPORT_CONTIGS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.VDJ_B_CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_REPORTER.VDJ_B_REPORTER.VLOUPE_PREPROCESS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_REPORTER.VDJ_T_REPORTER.SUMMARIZE_VDJ_REPORTS 2020-11-15 15:46:58 [runtime] (ready) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_REPORTER.VDJ_T_REPORTER.VLOUPE_PREPROCESS 2020-11-15 15:46:58 [runtime] (chunks_complete) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES 2020-11-15 15:46:58 [runtime] (chunks_complete) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION 2020-11-15 15:47:02 [runtime] (failed) ID.sn1.SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.DETECT_COUNT_CHEMISTRY
[error] Pipestance failed. Error log at: sn1/SC_RNA_COUNTER_CS/SC_MULTI_CS/SC_MULTI_CORE/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u9dccb14d71/_errors : Log message: An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample SRR6745454 in "/home/yoyolab/0_Public_data/1_scRNA/3_preimplantation/2_GSM2871123/0_fastq_dump". Please check your input data.
Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure.
2020-11-15 15:47:08 Shutting down. Martian Runtime - v4.0.0 Serving UI at http://liulab:35913?auth=5VBjah8-Vks9MFtDQejlNItVnXe6DTv7s2rBbQZKgYg `