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pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
https://www.kallistobus.tools/
BSD 2-Clause "Simplified" License
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kallisto index file not found index.idx_cdna #219

Closed feasiblee closed 10 months ago

feasiblee commented 11 months ago

Here, I found a question, please ask everyone, is Error: kallisto index file not found index.idx_cdna. Detailed description: kb count --h5ad -i index.idx_cdna,index.idx_intron.0,index.idx_intron.1,index.idx_intron.2,index.idx_intron.3,index.idx_intron.4,index.idx_intron.5,index.idx_intron.6,index.idx_intron.7 -g t2g.txt -x 10xv2 -o SRR6470907 -c1 spliced_t2c.txt -c2 unspliced_t2c.txt --workflow lamanno --filter bustools -t 2 \

SRR18516664_1.fastq.gz \ SRR18516664_2.fastq.gz [2023-10-13 01:02:00,174] INFO Generating BUS file using 9 indices [2023-10-13 01:02:00,175] INFO Using index index.idx_cdna to generate BUS file to SRR6470907/tmp/bus_part0 from [2023-10-13 01:02:00,175] INFO SRR18516664_1.fastq.gz [2023-10-13 01:02:00,175] INFO SRR18516664_2.fastq.gz [2023-10-13 01:02:00,183] ERROR kallisto 0.46.2 Generates BUS files for single-cell sequencing

Usage: kallisto bus [arguments] FASTQ-files

Required arguments: -i, --index=STRING Filename for the kallisto index to be used for pseudoalignment -o, --output-dir=STRING Directory to write output to -x, --technology=STRING Single-cell technology used

Optional arguments: -l, --list List all single-cell technologies supported -t, --threads=INT Number of threads to use (default: 1) -b, --bam Input file is a BAM file -n, --num Output number of read in flag column (incompatible with --bam) -k, --kmer Alignment is done per kmer --verbose Print out progress information every 1M proccessed reads

Error: kallisto index file not found index.idx_cdna

Yenaled commented 11 months ago

You should: 1) Upgrade to the latest version kb-python via pip install, 2) Run kb ref to create your new index, 3) Run kb count using that index

The "multiple indices" feature that you're using is something that we no longer support.

feasiblee commented 11 months ago

Thank you very much for your answer, thank you

You should: 1) Upgrade to the latest version kb-python via pip install, 2) Run kb ref to create your new index, 3) Run kb count using that index

The "multiple indices" feature that you're using is something that we no longer support.

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