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: 9851f5db75
WARN: Nextflow version 24.10.0 does not match workflow required version: 23.10.1 -- Execution will continue, but things may break!
.--:--:---.\
{} : {} : __ _ __ __ ____
||__"_|| : | || || \ / || __ \
/ \ `={}_ | N \ A| S Q || Q_| \
| NASQQ | ( ) |_| \_||_| V |_||_| \_|
| v1.0.0 | ( )
| ____ | ( ) Nextflow Automatization and Standarization for Qualitative and Quantitative
| | | | ( ) 1H 1D NMR metabolomics data preparation and analysis
|___|____|_| ( ) =======================================
| | ( ) input from : manifest.csv
/| || |\ ( ) output to : output/outdir_all
| | || | |( ) ------
| |____||____| |( ) run as : nextflow run ../main.nf -c ../nextflow.config -profile standard -params-file params.yml
| _________ |( ) started at : 2024-11-07T11:13:06.304956+01:00
| | | | | |( ) launchdir at : /Users/kkazimierczuk/Dropbox/Krzysztof/revisions/GIGAScience/nasqq
|__| |_| |_|(___)
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...)
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...)