cellranger count error:An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input

Question

[CRISPYCC]

An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample SRR11509941_LZ017_LZ018_LZ019 in "GSE149512/SRR11509941_LZ017_LZ018_LZ019_fastq". Please check your input data.

• 0.0% for chemistry SC5P-PE
• 0.0% for chemistry SC3Pv2
• 0.0% for chemistry SC3Pv3
• 0.0% for chemistry SC3Pv3HT
• 0.0% for chemistry SC3Pv3LT

i checked the R1,R2fastq, both length are 150nt,and i don't think it is the reason the code i use is correct because the other sample runs successfully please help me

[GenoMax]

It would help to provide the code you are using. Are the files correctly labeled as required?

[CRISPYCC]

like this?

10x/cellranger-7.2.0/cellranger count --sample SRR11616271_LZ005 --fastqs SRR11616271_LZ005_fastq --transcriptome gtf/01.10X_cellranger/human/GRCh38 --id SRR11616271_LZ005 > SRR11616271_LZ005.cellranger.log 2>&1

[GenoMax]

Show us the output of ls -1 SRR11616271_LZ005_fastq.

[CRISPYCC]

$ ls -1 SRR11509941_LZ017_LZ018_LZ019_S1_L001_R*
SRR11509941_LZ017_LZ018_LZ019_S1_L001_R1_001.fastq.gz
SRR11509941_LZ017_LZ018_LZ019_S1_L001_R2_001.fastq.gz

this is the sample which met the error

[GenoMax]

That is not quite what I had asked. Based on the command above are these files inside SRR11616271_LZ005_fastq directory? That is what is in the command line for cellranger.

[CRISPYCC]

i am sorry, i noticed the command i offered with LZ005sample went successfully, however when i change it into SRR11509941_LZ017_LZ018_LZ019 sample, the error just occurred. orz

[CRISPYCC]

$ 10x/cellranger-7.2.0/cellranger count --id SRR11509941_LZ017_LZ018_LZ019 --sample SRR11509941_LZ017_LZ018_LZ019 --fastqs SRR11509941_LZ017_LZ018_LZ019_fastq --localcores=12 --transcriptome gtf/01.10X_cellranger/human/GRCh38

Martian Runtime - v4.0.11 2024-09-28 15:17:55 [jobmngr] WARNING: configured to use 453GB of local memory, but only 412.6GB is currently available. 2024-09-28 15:17:56 [runtime] Reattaching in local mode. Serving UI at http://hello-PowerEdge-T640:46385?auth=ydWp_hUh0RgdXfg8FmD3y1_JCRNqrugvguhiHC6xAIc

2024-09-28 15:17:56 [runtime] (reset-partial) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0 2024-09-28 15:17:56 [runtime] (reset-partial) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0 2024-09-28 15:17:56 [runtime] (reset-partial) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX.fork0.chnk0 2024-09-28 15:17:56 [runtime] Found orphaned local stage: ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2024-09-28 15:17:56 [runtime] Found orphaned local stage: ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2024-09-28 15:17:56 [runtime] Found orphaned local stage: ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX 2024-09-28 15:17:56 [runtime] (split_complete) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX 2024-09-28 15:17:56 [runtime] (run:local) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX.fork0.chnk0.main 2024-09-28 15:17:56 [runtime] (split_complete) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2024-09-28 15:17:56 [runtime] (run:local) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2024-09-28 15:17:56 [runtime] (split_complete) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2024-09-28 15:17:56 [runtime] (run:local) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main 2024-09-28 15:18:15 [runtime] (failed) ID.SRR11509941_LZ017_LZ018_LZ019.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY

[error] Pipestance failed. Error log at: SRR11509941_LZ017_LZ018_LZ019/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u13cff7ada4/_errors

Log message: An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample SRR11509941_LZ017_LZ018_LZ019 in "/home/jialuqian/luqian/T_cell/00.data/pwj_data/02.Redo_normal10_NOA_GSE149512/SRR11509941_LZ017_LZ018_LZ019_fastq". Please check your input data.

• 0.0% for chemistry SC5P-PE
• 0.0% for chemistry SC3Pv2
• 0.0% for chemistry SC3Pv3
• 0.0% for chemistry SC3Pv3HT
• 0.0% for chemistry SC3Pv3LT

Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure.

2024-09-28 15:18:21 Shutting down. Saving pipestance info to "SRR11509941_LZ017_LZ018_LZ019/SRR11509941_LZ017_LZ018_LZ019.mri.tgz" For assistance, upload this file to 10x Genomics by running:

cellranger upload <your_email> "SRR11509941_LZ017_LZ018_LZ019/SRR11509941_LZ017_LZ018_LZ019.mri.tgz"