GA fails on macOS due to `Failed spawning readFilesCommand`

[eboileau]

I currently have no easy way to test STAR on macOS other than through GitHub Actions for my package. I'm currently updating supported Python versions. The first few lines of my workflow look like:

jobs:
  install-and-test:
    runs-on: ${{matrix.os}}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: ["3.11", "3.12", "3.13"]
    steps:
      - uses: actions/checkout@v5
      - uses: conda-incubator/setup-miniconda@v3

This worked before (3.7, 3.8, 3.9, and 3.10), although at some point I had to run legacy versions on Intel CPUs by forcing macos-13, instead of macos-latest.

STAR is installed

star                                  2.7.11b          haf7d672_7             bioconda

but it systematically fails to map under macOS (macos-15-arm64, I also tried macos-14-arm64, and the deprecated macos-13). Linux is fine, all tests complete successfully.

I include the relevant traceback below for one macOS run:

EXITING: because of fatal EXECUTION error: Failed spawning readFilesCommand
2: No such file or directory

Sep 23 13:08:53 ...... FATAL ERROR, exiting
Traceback (most recent call last):
  File "/Users/runner/miniconda3/envs/rpbp/bin/create-base-genome-profile", line 7, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/runner/miniconda3/envs/rpbp/lib/python3.12/site-packages/rpbp/orf_profile_construction/create_base_genome_profile.py", line 243, in main
    shell_utils.call_if_not_exists(
  File "/Users/runner/miniconda3/envs/rpbp/lib/python3.12/site-packages/pbiotools/misc/shell_utils.py", line 366, in call_if_not_exists
    ret_code = check_call(cmd, call=call, raise_on_error=raise_on_error)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/runner/miniconda3/envs/rpbp/lib/python3.12/site-packages/pbiotools/misc/shell_utils.py", line 202, in check_call
    return check_call_step(cmd, call=call, raise_on_error=raise_on_error)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/runner/miniconda3/envs/rpbp/lib/python3.12/site-packages/pbiotools/misc/shell_utils.py", line 184, in check_call_step
    raise subprocess.CalledProcessError(ret_code, cmd)
subprocess.CalledProcessError: Command 'STAR --runThreadN 1 --genomeDir /private/var/folders/q0/wmf37v850txck86cpnvwm_zw0000gn/T/pytest-of-runner/pytest-0/data0/c-elegans-chrI-example/WBcel235.79.chrI/star-index --sjdbGTFfile /private/var/folders/q0/wmf37v850txck86cpnvwm_zw0000gn/T/pytest-of-runner/pytest-0/data0/c-elegans-chrI-example/input/WBcel235.79.chrI.gtf --readFilesIn /private/var/folders/q0/wmf37v850txck86cpnvwm_zw0000gn/T/pytest-of-runner/pytest-0/data0/c-elegans-chrI-example/without-rrna/c-elegans-rep-1.fastq.gz  --readFilesCommand gzcat --limitBAMsortRAM 2147483648 --alignIntronMin 20 --alignIntronMax 100000 --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes AS NH HI nM MD --outSAMtype BAM SortedByCoordinate --sjdbOverhang 33 --seedSearchStartLmaxOverLread 0.5 --winAnchorMultimapNmax 100 --outFileNamePrefix /private/var/folders/q0/wmf37v850txck86cpnvwm_zw0000gn/T/pytest-of-runner/pytest-0/data0/c-elegans-chrI-example/without-rrna-mapping/c-elegans-rep-1' returned non-zero exit status 102.

I also tried with --readFilesCommand gunzip -c and --readFilesCommand "gunzip -c", without success. On Linux, I use --readFilesCommand zcat.

I don't really understand the error, whether STAR fails to read the readFilesCommand's argument, whether the argument is not a valid command on macOS, or if there is actually something else preventing it from spawning some process...

As far as I can tell, all previous steps run fine, the files and index should be there.

Any piece of advice is appreciated. Thanks.

[eboileau]

It doesn't seem related to the readFilesCommand's argument, at least I made sure that on macOS, whether it's gunzip -c or gzcat, its installed and available on the $PATH, from the conda environment and globally. But even when visible it doesn't seem to guarantee that it can be used by STAR as a child process... STAR fails with the same error.

macOS sandboxing or security policies + Conda + GitHub Actions ?? I really don't know how to test this...

[andi-bergeson]

Hey there, same conditions & error, did you end up figuring out why readFilesCommand triggers this?

[aryazand]

Hi, I am having the same issue using the star snakemake wrapper. I am on a Macos as well. Does anybody have solutions?

[husensofteng]

the same here, installed STAR via conda. it works if extract the fastq but not with any of the zip commands in readFilesCommand

[S00NYI]

I've been having similar issue, I reverted STAR to 2.7.10b from 2.7.11b and it seems to be working fine now. Currenly on macOS Tahoe 26.2.

[erzakiev]

I've been having similar issue, I reverted STAR to 2.7.10b from 2.7.11b and it seems to be working fine now. Currenly on macOS Tahoe 26.2.

how did you rollback to 2.7.10b? There's no osx-arm64 version for that build on conda.

[S00NYI]

I've been having similar issue, I reverted STAR to 2.7.10b from 2.7.11b and it seems to be working fine now. Currenly on macOS Tahoe 26.2.

how did you rollback to 2.7.10b? There's no osx-arm64 version for that build on conda.

Try the following, just tested on a different conda environment:
CONDA_SUBDIR=osx-64 mamba install -y bioconda::star=2.7.10b