Closed bjhardcastle closed 7 months ago
Workflow exited with the following error:
N E X T F L O W ~ version 22.10.0 Launching `main.nf` [comp-26c8af68-0b43-45ab-9d3d-32c5c25] DSL1 - revision: c8d71b5fa9 [05/1f9e57] Submitted process > capsule_nwb_packaging_subject_capsule_10 (capsule-1748641) [5c/c481ad] Submitted process > capsule_aind_ephys_job_dispatch_4 (capsule-5089190) Error executing process > 'capsule_nwb_packaging_subject_capsule_10 (capsule-1748641)' Caused by: Essential container in task exited Command executed: #!/usr/bin/env bash set -e export CO_CAPSULE_ID=dde17e00-2bad-4ceb-a00e-699ec25aca64 export CO_CPUS=4 export CO_MEMORY=34359738368 mkdir -p capsule mkdir -p capsule/data && ln -s $PWD/capsule/data /data mkdir -p capsule/results && ln -s $PWD/capsule/results /results mkdir -p capsule/scratch && ln -s $PWD/capsule/scratch /scratch echo "[capsule-1748641] cloning git repo..." git clone "https://$GIT_ACCESS_TOKEN@codeocean.allenneuraldynamics.org/capsule-1748641.git" capsule-repo git -C capsule-repo checkout 9dc8a496f86fe38250d584b8e3d396581b7e404b --quiet mv capsule-repo/code capsule/code rm -rf capsule-repo echo "[capsule-1748641] running capsule..." cd capsule/code chmod +x run ./run echo "[capsule-1748641] completed!" Command exit status: 1 Command output: [capsule-1748641] cloning git repo... [capsule-1748641] running capsule... Backend: zarr Asset name: ecephys_626791_2022-08-17_00-00-00 Command error: [capsule-1748641] cloning git repo... Cloning into 'capsule-repo'... [capsule-1748641] running capsule... + python -u run_capsule.py Backend: zarr Asset name: ecephys_626791_2022-08-17_00-00-00 Traceback (most recent call last): File "/tmp/nxf.ApkO7rHLYv/capsule/code/run_capsule.py", line 182, in <module> run() File "/tmp/nxf.ApkO7rHLYv/capsule/code/run_capsule.py", line 153, in run species=subject_metadata["species"]["name"], TypeError: string indices must be integers Work dir: s3://codeocean-s3batchbucket-16itpvq060udk/1f8f159a-7670-47a9-baf1-078905fc9c2e/05/1f9e57cfc34ba211b0adf807a8637b Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
I'm guessing this is a metadata schema issue, where subject_metadata["species"] is a str in older versions and a dict in newer versions.
subject_metadata["species"]
Yep, fixed here. Can you try to rerun the session?
Thanks for the quick fix. Re-running now
Fixed
Workflow exited with the following error:
I'm guessing this is a metadata schema issue, where
subject_metadata["species"]
is a str in older versions and a dict in newer versions.