kb info returns non-zero exit status

[yamanq]

Describe the issue kb info returns a non-zero exit status, which is unexpected since no errors occurred and no undefined syntax was used.

What is the exact command that was run?

kb info
echo $?

Command output (with --verbose flag)

> kb info --verbose
kb_python 0.27.3
kallisto: 0.48.0 (/tmp/tmp.889zeieDYs/env/lib/python3.10/site-packages/kb_python/bins/linux/kallisto/kallisto)
bustools: 0.41.0 (/tmp/tmp.889zeieDYs/env/lib/python3.10/site-packages/kb_python/bins/linux/bustools/bustools)
kb is a python package for rapidly pre-processing single-cell RNA-seq data. It
is a wrapper for the methods described in [2].

The goal of the wrapper is to simplify downloading and running of the kallisto
[1] and bustools [2] programs. It was inspired by Sten Linnarsson’s loompy
fromfq command (http://linnarssonlab.org/loompy/kallisto/index.html)

The kb program consists of two parts:

The `kb ref` command builds or downloads a species-specific index for
pseudoalignment of reads. This command must be run prior to `kb count`, and it
runs the `kallisto index` [1].

The `kb count` command runs the kallisto [1] and bustools [2] programs. It can
be used for pre-processing of data from a variety of single-cell RNA-seq
technologies, and for a number of different workflows (e.g. production of gene
count matrices, RNA velocity analyses, etc.). The output can be saved in a
variety of formats including mix and loom. Examples are provided below.

Examples are available at: https://www.kallistobus.tools/tutorials

References
==========
[1] Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal
probabilistic RNA-seq quantification. Nature biotechnology, 34(5), 525.
[2] Melsted, P., Booeshaghi, A. S., Liu, L., Gao, F., Lu, L., Min, K. H., da
Veiga Beltrame, E., Hjorleifsson, K. E., Gehring, J., & Pachter, L. (2021).
Modular and efficient pre-processing of single-cell RNA-seq. Nature
Biotechnology.
> echo $?
1

[github-actions[bot]]

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days

[yamanq]

This is still an issue.