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OSError: truncated file is occured in cellranger-5.0.1-dirty output. #387

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ilovegreentea opened this issue Feb 26, 2024 · 0 comments
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@ilovegreentea
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Error:: below error is occured when running velocyto with cellranger-5.0.1-dirty. with cellranger 7.0.0 version is OK.

OSError: truncated file
[E::bgzf_uncompress] CRC32 checksum mismatch
[E::bgzf_read_block] BGZF decode jobs returned error 1 for block offset 17210303020
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
samtools sort: truncated file. Aborting

I don't know why this Error occured..
please give me any advice for this.

version ::
samtools 1.19.2
Using htslib 1.19.1
velocyto : 0.17.17

I used like this.
velocyto run -b /mypath/outs/filtered_feature_bc_matrix/barcodes.tsv.gz -o /mypath/result/ /mypath/outs/possorted_genome_bam.bam /mypath/refdata-gex-GRCh38-2020-A/genes/genes.gtf

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