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zamboni-lab / SLAW

Scalable and self-optimizing processing workflow for untargeted LC-MS
GNU General Public License v2.0
27 stars 3 forks source link

processing halted #35

Closed Sunshine318 closed 2 months ago

Sunshine318 commented 1 year ago

All the files ran through processing . Individual csv files created and individual MSMS mgf files created . Program is halted at this step and not running any further. No pdf file created nor any data matrices in the datamatrice folder "2023-11-04|00:54:51|DEBUG: stderr:Warning message: In file.remove(feature_ml) : cannot remove file '/output/OPENMS/peaktables/peaktable_1220_17ecec2598750e8a40 cannot remove file '/output/OPENMS/peaktables/peaktable_1220_17ecec2598750e8a40dca308cb44d5c4.featureXML', reason 'No such file or directory' 2023-11-04|00:54:51|DEBUG: Rscript /pylcmsprocessing/Rscript/FromFeaturesMLToDf.R "/output/OPENMS/peaktables/peaktable_1221_94248c3ae559fde15fb5797e9a31c289.featureXML" "/output/OPENMS/peaktables/peaktable_1221_94248c3ae559fde15fb5797e9a31c289.csv" 2023-11-04|00:55:07|DEBUG: Rscript /pylcmsprocessing/Rscript/FromFeaturesMLToDf.R "/output/OPENMS/peaktables/peaktable_1280_1867a768fa8e554e363e79a91a9f6823.featureXML" "/output/OPENMS/peaktables/peaktable_1280_1867a768fa8e554e363e79a91a9f6823.csv" 2023-11-04|01:01:29|DEBUG: Rscript /pylcmsprocessing/Rscript/FromFeaturesMLToDf.R "/output/OPENMS/peaktables/peaktable_1222_1ec74d7f542b2cd66cbc157945b4cf45.featureXML" "/output/OPENMS/peaktables/peaktable_1222_1ec74d7f542b2cd66cbc157945b4cf45.csv" 2023-11-04|01:05:02|DEBUG: Rscript /pylcmsprocessing/Rscript/FromFeaturesMLToDf.R "/output/OPENMS/peaktables/peaktable_1223_1afea92b195ebae8b78ad5d009800d79.featureXML" "/output/OPENMS/peaktables/peaktable_1223_1afea92b195ebae8b78ad5d009800d79.csv" 2023-11-04|01:09:16|DEBUG: Rscript /pylcmsprocessing/Rscript/FromFeaturesMLToDf.R "/output/OPENMS/peaktables/peaktable_1224_669e7488b018036210d28bbf28ef1a8b.featureXML" "/output/OPENMS/peaktables/peaktable_1224_669e7488b018036210d28bbf28ef1a8b.csv" 2023-11-04|01:12:59|DEBUG: Rscript /pylcmsprocessing/Rscript/extractingMGFfromMZML.R "/output/temp_processing_db.sqlite" "/output/OPENMS/msms" 0.0 5 True 2023-11-04|01:20:59|DEBUG: stdout:Extracting all MS-MS spectra. 2023-11-04|01:20:59|DEBUG: stderr:Linking to: OpenSSL 1.1.1f 31 Mar 2020 MS-MS spectra extraction finished 2023-11-04|01:20:59|INFO: MS2 extraction finished 2023-11-04|01:21:01|INFO: Starting peaktable filtration 2023-11-04|01:25:51|INFO: Done peaktables filtration 2023-11-04|01:25:51|INFO: STEP: peakpicking TOTAL_TIME:275486.76s LAST_STEP:275484.83s 2023-11-04|01:25:51|INFO: Aligning 2023-11-04|01:25:51|DEBUG: Rscript /pylcmsprocessing/Rscript/construct_peaktable_online.R "/output/temp_processing_db.sqlite" "/output/temp/blocks" "/output/temp/alignement.rds" "/output/datamatrices/datamatrix_fc9ed745628d36db1c9f5ff4ffcd0ab2.csv" intensity 0.03 0.01 15.0 150 0.1 2 "/output/figurefc9ed745628d36db1c9f5ff4ffcd0ab2.pdf""

Sunshine318 commented 9 months ago

Only MS2 extraction is finished and fused mgf folder is created but no fused mgf file is created and no files in datamatrices folder.

Sunshine318 commented 9 months ago

2024-01-17|23:21:20|INFO: Total memory available: 67603 and 72 cores. The workflow will use 952 Mb by core on 71 cores. 2024-01-17|23:21:20|INFO: Guessing polarity from file:20200227-EX01010-A003-IN0028-S00044243-PM3118-P.mzML 2024-01-17|23:21:31|INFO: Polarity detected: positive 2024-01-17|23:21:34|INFO: STEP: initialisation TOTAL_TIME:14.58s LAST_STEP:14.58s 2024-01-17|23:21:37|INFO: 564 peakpicking added 2024-01-18|00:24:55|INFO: MS2 extraction finished 2024-01-18|00:24:57|INFO: Starting peaktable filtration 2024-01-18|00:25:06|INFO: Done peaktables filtration 2024-01-18|00:25:06|INFO: STEP: peakpicking TOTAL_TIME:3825.76s LAST_STEP:3811.18s 2024-01-18|00:25:06|INFO: Aligning 2024-01-18|00:25:24|INFO: Filtering 2024-01-18|00:25:25|INFO: Extracting consensus MS-MS spectra 2024-01-18|00:25:32|INFO: Alignment finished 2024-01-18|00:25:32|INFO: STEP: alignment TOTAL_TIME:3852.43s LAST_STEP:26.68s 2024-01-18|00:25:32|INFO: Gap filling and isotopic pattern extraction finished. 2024-01-18|00:25:32|INFO: STEP: gap-filling TOTAL_TIME:3852.45s LAST_STEP:0.01s 2024-01-18|00:25:32|INFO: Annotation finished 2024-01-18|00:25:32|INFO: STEP: annotation TOTAL_TIME:3852.47s LAST_STEP:0.03s [tanusoni@gl-login3 ~]$

No fused mgf or datamatrices files created