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labsyspharm / ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
https://labsyspharm.github.io/ashlar/
MIT License
126 stars 42 forks source link

Output directory '[output path]' does not exist #156

Open thaopcao opened 2 years ago

thaopcao commented 2 years ago

Previously, we were able to use a bash script and run Ashlar on Linux using:

ashlar "${c[@]}" --pyramid --flip-y --maximum-shift $MAX_SHIFT --filter-sigma $SIGMA --align-channel $ALIGN_CHANNEL -o $OUTPUT_DIR"image_1".ome.tiff

ASHLAR would reach the input files (ome.tiff) in c[@] and create a single pyramidal output file (image_1.ome.tiff) in the output_dir directory.

However, when running today, ASHLAR returned this error: Output directory '[output path]' does not exist. Has anyone encountered the same issue? I'd truly appreciate your help and time. Thank you!

jmuhlich commented 1 year ago

Does the directory referenced in your $OUTPUT_DIR variable exist? Ashlar will not create any directories for you, so the full path to the file named in the -o option must exist already. Does the error literally say '[output path]' or an actual path? That error message reports the path to the directory you provided in -o so if it literally says '[output path]' then I think you should check your bash script.