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pachterlab / BYVSTZP_2020

This repository contains the code for reproducing all the results and figures from the preprint "Isoform specificity in the mouse primary motor cortex".
BSD 2-Clause "Simplified" License
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abundance file not generated #7

Closed jkniehaus closed 2 years ago

jkniehaus commented 2 years ago

Hi @sbooeshaghi, I'm trying to quantify multiple paired-end fastq files from single-cell smartseq data similar to what was done in the corresponding publication . I'm experiencing an issue with quantification of a batch (testing n=2 cells) fastq files where kallisto pseudo --quant does not provide the abundance matrix needed to generate a cells x transcripts matrix.

The kallisto pseudo --quant with -b batch option + file either does not recognize the --quant command (pseudo: unrecognized option '--quant'; v0.44.0), or I get a segmentation error: [quant] finding pseudoalignments for all files .../var/spool/slurmd/job35157683/slurm_script: line 4: 251503 Segmentation fault (v0.43.1 & v0.46.1).

The command I'm using is: kallisto pseudo --quant -i /path/to/transcriptome.idx -o kallisto/out/ -b seq_batch.txt -t 8

Any guidance would be a big help.

Thanks!

sbooeshaghi commented 2 years ago

Hey Jesse, can you try updating kallisto to 0.46.2?

https://github.com/pachterlab/kallisto/releases/tag/v0.46.2

If you still run into problems please let me know!

jkniehaus commented 2 years ago

Worked like a charm! Forgive my naivety, probably should've checked that first. Thanks!