lukpru
commented
2 weeks ago Hello,
I have a few suggestions:
- Please install the required version of Nextflow (your current version is 24.10.0, but 24.10.1 is needed).
- Try building the Docker image directly from the Dockerfile, as outlined in the Project Setup section of the README.
- Use the previous version of Docker and tag it as latest, as some packages were recently updated. You can do this with the following commands:
docker pull ghcr.io/ardigen/nasqq/r_utils:1.0.0
docker tag ghcr.io/ardigen/nasqq/r_utils:1.0.0 ghcr.io/ardigen/nasqq/r_utils:latest
- Consider running the pipeline on a Linux machine, as there may be issues with memory allocation on macOS.
After the recent update to version 1.1, which includes extra steps such as batch correction, special case handling in multivariate analysis, and additional parameters for workflow control, the execution time has increased significantly. Depending on the machine, it may now take 2-3 times longer (up to 8 hours). This is an issue I plan to address in the next pipeline release (v1.2).
kkazi1980
HelloI
I tried to rerun the program under MacOS (Sequoia 15.0). Environment: java 21.0.4 2024-07-16 LTS nextflow 24.10.0 Docker version 27.3.1, build ce12230
On the test data, it stops progressing on the metabolite quantification step (I used the test data from GitHub):
nextflow run ../main.nf -c ../nextflow.config -profile standard -params-file params.yml
N E X T F L O W ~ version 24.10.0
Launching
../main.nf[loving_faggin] DSL2 - revision: 9851f5db75WARN: Nextflow version 24.10.0 does not match workflow required version: 23.10.1 -- Execution will continue, but things may break!
executor > local (44) [4b/7eac28] SPECTRAL_PREPROCESSING:LOAD_FIDS (test2) [100%] 3 of 3 ✔ [db/5b974c] SPECTRAL_PREPROCESSING:RAW_FIDS_VISUALIZATION (test2) [100%] 3 of 3 ✔ [0f/062a0a] SPECTRAL_PREPROCESSING:GROUP_DELAY_CORRECTION (test2) [100%] 3 of 3 ✔ [59/6fe90e] SPECTRAL_PREPROCESSING:SOLVENT_SUPPRESSION (test2) [100%] 3 of 3 ✔ [ff/df57ca] SPECTRAL_PREPROCESSING:APODIZATION (test2) [100%] 3 of 3 ✔ [13/3a575b] SPECTRAL_PREPROCESSING:ZERO_FILLING (test2) [100%] 3 of 3 ✔ [ee/d0704e] SPECTRAL_PREPROCESSING:FOURIER_TRANSFORMATION (test2) [100%] 3 of 3 ✔ [06/df42e6] SPECTRAL_PREPROCESSING:ZERO_ORDER_PHASE_CORRECTION (test2) [100%] 3 of 3 ✔ [18/86ae70] SPECTRAL_PREPROCESSING:INTERNAL_REFERENCING (test2) [100%] 3 of 3 ✔ [9b/cb6b59] SPECTRAL_PREPROCESSING:BASELINE_CORRECTION (test2) [100%] 3 of 3 ✔ [06/8c1843] SPECTRAL_PREPROCESSING:NEGATIVE_VALUES_ZEROING (test2) [100%] 3 of 3 ✔ [a3/d70ce9] SPECTRAL_PREPROCESSING:WARPING (test2) [100%] 3 of 3 ✔ [19/0175f2] SPECTRAL_PREPROCESSING:WINDOW_SELECTION (test3) [ 66%] 2 of 3 [6d/b1bf51] SPECTRAL_PREPROCESSING:BUCKETING (test3) [100%] 2 of 2 [14/dbcda9] SPECTRAL_PREPROCESSING:NORMALIZATION (test3) [100%] 2 of 2 [02/a62182] METABOLITES_QUANTIFICATION (test3) [ 50%] 1 of 2 [- ] ADD_METADATA [ 0%] 0 of 1 [- ] COMBINE_DATASET_BATCHES - [- ] DATA_ANALYSIS:FEATURES_PROCESSING - [- ] DATA_ANALYSIS:EXPLORATORY_DATA_ANALYSIS - Plus 4 more processes waiting for tasks…
The code stays here forever (5 hours now...)