Comments (2)
zqzneptune
commented on July 26, 2024
We are experiencing the same issue. The number of cells to be processed is ~10K.
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Hoohm
commented on July 26, 2024
I would try and run with fewer cores, maybe something like 4 to 8.
50k cells should be fine. Not sure what's going on there. Can you try the https://github.com/Hoohm/CITE-seq-Count/tree/feature/cells_argument branch?
It's a new implementation. Sadly it's worse in terms of memory, but it might survive your bug.
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Related Issues (20)
- Different "UMIs corrected" results between v1.4.3 and v1.4.5 HOT 2
- Code for running multiple lanes
- ValueError: columns cannot be a set HOT 5
- Cell Hashing on Multiome samples HOT 11
- bug in preprocessing.py -> get_read_paths() (version 1.4.3) HOT 1
- method keeps looking for whitelist when not provided. HOT 8
- 100% unmapped
- Discussion question -- is it normal to take so long? HOT 3
- Include path to tag file in run report HOT 1
- barcodes with 0s in all protein tags and unmapped roll HOT 2
- Running Cite-Seq-count with next GEM protocol HOT 2
- Pandas error after correcting UMIs HOT 1
- Allow to split fastq or get list of readID per cell HOT 2
- Unable to locate temp file while merging results
- Does not compile using Python version > 3.9.x please fix.
- Gene and Antibody both have a pair of fastq files, how to run CITE-seq-Count?
- Please, trim all sequences at the same length.
- CITE-seq-Count run gets stuck
- ValueError: columns cannot be a set HOT 3
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