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invalid utf-8 parsing error in cellranger multi #257

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YohannesMuTa opened this issue Mar 28, 2025 · 1 comment
Closed

invalid utf-8 parsing error in cellranger multi #257

YohannesMuTa opened this issue Mar 28, 2025 · 1 comment

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@YohannesMuTa
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YohannesMuTa commented Mar 28, 2025

I am working with cellranger 7.2.0
I am having an error copied below. I inspected my multi_config.csv(here gem2_new.csv) and recreated multiple versions in UTF-8 format, but I could not solve the problem. Any idea on what I can do? Thanks

davidvteam@ulb-System-Product-Name:~/horus_outs$ cellranger multi --id GEM2 --csv /home/davidvteam/dvsc/references/multi_files/multi_config_files_horus/gem2_new.csv

Martian Runtime - v4.0.11
Serving UI at ###########@@@@@#####

Running preflight checks (please wait)...

[error] Pipestance failed. Error log at:
GEM2/SC_MULTI_CS/MULTI_PREFLIGHT_LOCAL/fork0/chnk0-u3b51e6d325/_errors

Log message:
CSV parse error: record 8 (line 8, field: 0, byte: 578):

gem2_new.csv

: invalid UTF-8 in field 0 near byte index 4

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

2025-03-28 17:49:53 Shutting down.
Saving pipestance info to "GEM2/GEM2.mri.tgz"
For assistance, upload this file to 10x Genomics by running:

cellranger upload <your_email> "GEM2/GEM2.mri.tgz"

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Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Mar 28, 2025
@github-actions github-actions bot locked and limited conversation to collaborators Mar 28, 2025
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