Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries

SunRisingYang commented 3 months ago

Hi there,

I'm encountering some errors when running CellRanger with the data you provided, specifically the sample labeled 'FCA_GND8103053'. It's worth noting that I've tested the process with other datasets and haven't encountered this issue. Could you kindly verify that the sample 'FCA_GND8103053' is correct and free from any known issues?

Thank you in advance for your help.

[error] Pipestance failed. Error log at: FCA_GND8103053/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u38c2a5d043/_errors

Log message: Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for Sample FCA_GND8103053 in "/public2/home/rotation/yangxusheng/scRNASeq/data/human/rawdata/9PCW_Female". Total Reads = 100000 Mapped reads = 68170 Sense reads = 16837 Antisense reads = 22086

In order to distinguish between the 3' vs 5' assay configuration the following conditions need to be satisfied:

A minimum of 1000 confidently mapped reads
A minimum of 5.0% of the total reads considered needs to be confidently mapped
The number of sense reads need to be at least 2x compared to the antisense reads or vice versa

Please validate the inputs and/or specify the chemistry via the --chemistry argument.

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

2024-07-28 13:00:58 Shutting down. Saving pipestance info to "FCA_GND8103053/FCA_GND8103053.mri.tgz" For assistance, upload this file to 10x Genomics by running:

cellranger upload "FCA_GND8103053/FCA_GND8103053.mri.tgz"

luzgaral commented 3 months ago

Hi @SunRisingYang

Can you confirm your data source please?

Best,

Luz

SunRisingYang commented 3 months ago

Thank you for your prompt reply! Yes, I have successfully downloaded the data from the FTP link ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR968/ERR9681812, and I have verified its integrity by comparing the MD5 checksum to ensure that the download was complete and undamaged. Best.

handsomeluegg commented 2 months ago

Hi, I encountered the same issue while using cellranger count. I was wondering if you were able to resolve it? Thanks!

ventolab / HGDA

Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries #4