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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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PgrGet() error in regenie step 2 #481

Open dianacornejo opened 11 months ago

dianacornejo commented 11 months ago

Hi @joellembatchou I'm trying to run regenie using the RAP system for UKB data. I have a WDL workflow created for this and was working fine while using bgen files as input. However I'm getting this error (this is an example for one chromosome but can happen in others..and interestingly some of those jobs per chromosome do finish successfully)

Cause of Failure
job script function run_command exited with permanent fail code 255 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4 PgrGet1() error 4

When using the corresponding pgen files (generated using plink)

This is the full log file. Do you have any idea on what may be happening?. I'm unsure how to debug this. Thanks in advance

[Dec 14 2023, 3:37 PM] 
[Dec 14 2023, 3:37 PM]               |=============================|
[Dec 14 2023, 3:37 PM]               |      REGENIE v3.2.6.gz      |
[Dec 14 2023, 3:37 PM]               |=============================|
[Dec 14 2023, 3:37 PM] 
[Dec 14 2023, 3:37 PM] Copyright (c) 2020-2022 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
[Dec 14 2023, 3:37 PM] Distributed under the MIT License.
[Dec 14 2023, 3:37 PM] Compiled with Boost Iostream library.
[Dec 14 2023, 3:37 PM] 
[Dec 14 2023, 3:37 PM] Log of output saved in file : ukb23157_c19.concat.log
[Dec 14 2023, 3:37 PM] 
[Dec 14 2023, 3:37 PM] WARNING: option --firth will not be applied (it is only run with binary traits).
[Dec 14 2023, 3:37 PM] Options in effect:
[Dec 14 2023, 3:37 PM]   --step 2 \
[Dec 14 2023, 3:37 PM]   --threads 16 \
[Dec 14 2023, 3:37 PM]   --pgen /home/dnanexus/mnt/input0afaeb03-aa8b-4b38-94ae-704b4dbe8030/ukb23157_c19.concat \
[Dec 14 2023, 3:37 PM]   --phenoFile /home/dnanexus/inputs/input3310673543010783499/test.pheno \
[Dec 14 2023, 3:37 PM]   --covarFile /home/dnanexus/inputs/input3310673543010783499/test.covar \
[Dec 14 2023, 3:37 PM]   --pred /home/dnanexus/inputs/input3310673543010783499/fit_bin_out_pred.list \
[Dec 14 2023, 3:37 PM]   --bsize 1000 \
[Dec 14 2023, 3:37 PM]   --out ukb23157_c19.concat
[Dec 14 2023, 3:37 PM] 
[Dec 14 2023, 3:37 PM] Association testing mode with fast multithreading using OpenMP
[Dec 14 2023, 3:37 PM]  * pvar             : [/home/dnanexus/mnt/input0afaeb03-aa8b-4b38-94ae-704b4dbe8030/ukb23157_c19.concat.pvar] n_snps = 1654479
[Dec 14 2023, 3:37 PM]  * psam             : [/home/dnanexus/mnt/input0afaeb03-aa8b-4b38-94ae-704b4dbe8030/ukb23157_c19.concat.psam] n_samples = 469835
[Dec 14 2023, 3:37 PM]  * pgen             : [/home/dnanexus/mnt/input0afaeb03-aa8b-4b38-94ae-704b4dbe8030/ukb23157_c19.concat.pgen] 
[Dec 14 2023, 3:37 PM]  * phenotypes       : [/home/dnanexus/inputs/input3310673543010783499/test.pheno] n_pheno = 1
[Dec 14 2023, 3:37 PM]    -dropping observations with missing values at any of the phenotypes
[Dec 14 2023, 3:37 PM]    -number of phenotyped individuals with no missing data = 136540
[Dec 14 2023, 3:37 PM]  * covariates       : [/home/dnanexus/inputs/input3310673543010783499/test.covar] n_cov = 14
[Dec 14 2023, 3:37 PM]    -number of individuals with covariate data = 136540
[Dec 14 2023, 3:37 PM]  * number of individuals used in analysis = 136540
[Dec 14 2023, 3:37 PM]  * number of observations for each trait:
[Dec 14 2023, 3:37 PM]    - 'FEV1_FVC_RATIO': 136540 observations
[Dec 14 2023, 3:37 PM]  * LOCO predictions : [/home/dnanexus/inputs/input3310673543010783499/fit_bin_out_pred.list]
[Dec 14 2023, 3:37 PM]    -file [/home/dnanexus/work/fit_bin_out_1.loco] for phenotype 'FEV1_FVC_RATIO'
[Dec 14 2023, 3:37 PM]    -residualizing and scaling phenotypes...done (11ms) 
[Dec 14 2023, 3:37 PM]  * # threads        : [16]
[Dec 14 2023, 3:37 PM]  * block size       : [1000]
[Dec 14 2023, 3:37 PM]  * # blocks         : [1655]
[Dec 14 2023, 3:37 PM]  * approximate memory usage : 8GB
[Dec 14 2023, 3:37 PM]  * using minimum MAC of 5 (variants with lower MAC are ignored)
[Dec 14 2023, 3:37 PM] 
[Dec 14 2023, 3:37 PM] Chromosome 19 [1655 blocks in total]
[Dec 14 2023, 3:37 PM]    -reading loco predictions for the chromosome...done (134ms) 
[Dec 14 2023, 3:37 PM]  block [1/1655] : done (7325ms) 
[Dec 14 2023, 3:37 PM]  block [2/1655] : done (7021ms) 
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[Dec 14 2023, 3:43 PM] CPU: 21% (16 cores) * Memory: 9657/62826MB * Storage: 16/562GB * Net: 8↓/0↑MBps
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[Dec 14 2023, 3:53 PM] CPU: 31% (16 cores) * Memory: 15183/62826MB * Storage: 16/562GB * Net: 0↓/0↑MBps
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[Dec 14 2023, 4:03 PM] CPU: 31% (16 cores) * Memory: 11605/62826MB * Storage: 16/562GB * Net: 1↓/0↑MBps
[Dec 14 2023, 4:03 PM]  block [219/1655] : done (7191ms) 
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[Dec 14 2023, 4:04 PM]  block [225/1655] : done (6965ms) 
[Dec 14 2023, 4:04 PM]  block [226/1655] : done (6895ms) 
[Dec 14 2023, 4:04 PM]  block [227/1655] : done (7038ms) 
[Dec 14 2023, 4:04 PM]  block [228/1655] : done (6918ms) 
[Dec 14 2023, 4:04 PM]  block [229/1655] : done (7592ms) 
[Dec 14 2023, 4:05 PM]  block [230/1655] : done (7105ms) 
[Dec 14 2023, 4:05 PM]  block [231/1655] : done (6897ms) 
[Dec 14 2023, 4:05 PM]  block [232/1655] : done (7079ms) 
[Dec 14 2023, 4:05 PM]  block [233/1655] : done (7193ms) 
[Dec 14 2023, 4:05 PM]  block [234/1655] : done (6563ms) 
[Dec 14 2023, 4:05 PM]  block [235/1655] : done (7016ms) 
[Dec 14 2023, 4:05 PM]  block [236/1655] : done (7033ms) 
[Dec 14 2023, 4:05 PM]  block [237/1655] : done (6938ms) 
[Dec 14 2023, 4:05 PM]  block [238/1655] : done (7990ms) 
[Dec 14 2023, 4:06 PM]  block [239/1655] : done (7330ms) 
[Dec 14 2023, 4:06 PM]  block [240/1655] : done (7579ms) 
[Dec 14 2023, 4:06 PM]  block [241/1655] : done (7344ms) 
[Dec 14 2023, 4:06 PM]  block [242/1655] : done (6890ms) 
[Dec 14 2023, 4:06 PM]  block [243/1655] : done (7269ms) 
[Dec 14 2023, 4:06 PM]  block [244/1655] : done (7034ms) 
[Dec 14 2023, 4:06 PM]  block [245/1655] : done (6950ms) 
[Dec 14 2023, 4:06 PM]  block [246/1655] : done (7175ms) 
[Dec 14 2023, 4:07 PM]  block [247/1655] : done (6901ms) 
[Dec 14 2023, 4:07 PM]  block [248/1655] : done (7062ms) 
[Dec 14 2023, 4:07 PM]  block [249/1655] : done (7123ms) 
[Dec 14 2023, 4:07 PM]  block [250/1655] : done (7152ms) 
[Dec 14 2023, 4:07 PM]  block [251/1655] : done (7381ms) 
[Dec 14 2023, 4:07 PM]  block [252/1655] : done (6887ms) 
[Dec 14 2023, 4:07 PM]  block [253/1655] : done (7053ms) 
[Dec 14 2023, 4:07 PM]  block [254/1655] : done (6999ms) 
[Dec 14 2023, 4:07 PM]  block [255/1655] : done (6900ms) 
[Dec 14 2023, 4:08 PM]  block [256/1655] : done (7071ms) 
[Dec 14 2023, 4:08 PM]  block [257/1655] : done (7472ms) 
[Dec 14 2023, 4:08 PM]  block [258/1655] : done (7170ms) 
[Dec 14 2023, 4:08 PM]  block [259/1655] : done (6955ms) 
[Dec 14 2023, 4:08 PM]  block [260/1655] : done (6901ms) 
[Dec 14 2023, 4:08 PM]  block [261/1655] : done (6885ms) 
[Dec 14 2023, 4:08 PM]  block [262/1655] : done (6826ms) 
[Dec 14 2023, 4:08 PM]  block [263/1655] : done (6817ms) 
[Dec 14 2023, 4:09 PM]  block [264/1655] : done (7009ms) 
[Dec 14 2023, 4:09 PM]  block [265/1655] : done (6653ms) 
[Dec 14 2023, 4:09 PM]  block [266/1655] : done (7274ms) 
[Dec 14 2023, 4:09 PM]  block [267/1655] : done (7216ms) 
[Dec 14 2023, 4:09 PM]  block [268/1655] : done (7271ms) 
[Dec 14 2023, 4:09 PM]  block [269/1655] : done (6960ms) 
[Dec 14 2023, 4:09 PM]  block [270/1655] : done (6748ms) 
[Dec 14 2023, 4:09 PM]  block [271/1655] : done (6976ms) 
[Dec 14 2023, 4:09 PM]  block [272/1655] : done (7243ms) 
[Dec 14 2023, 4:10 PM]  block [273/1655] : done (7146ms) 
[Dec 14 2023, 4:10 PM]  block [274/1655] : done (7472ms) 
[Dec 14 2023, 4:10 PM]  block [275/1655] : done (7456ms) 
[Dec 14 2023, 4:10 PM]  block [276/1655] : done (7132ms) 
[Dec 14 2023, 4:10 PM]  block [277/1655] : done (6811ms) 
[Dec 14 2023, 4:10 PM]  block [278/1655] : done (7543ms) 
[Dec 14 2023, 4:10 PM]  block [279/1655] : done (7231ms) 
[Dec 14 2023, 4:10 PM]  block [280/1655] : done (7324ms) 
[Dec 14 2023, 4:11 PM]  block [281/1655] : done (7268ms) 
[Dec 14 2023, 4:11 PM]  block [282/1655] : done (7047ms) 
[Dec 14 2023, 4:11 PM]  block [283/1655] : done (7135ms) 
[Dec 14 2023, 4:11 PM]  block [284/1655] : done (7012ms) 
[Dec 14 2023, 4:11 PM]  block [285/1655] : done (7052ms) 
[Dec 14 2023, 4:11 PM]  block [286/1655] : done (10900ms) 
[Dec 14 2023, 4:11 PM]  block [287/1655] : done (7443ms) 
[Dec 14 2023, 4:11 PM]  block [288/1655] : done (7308ms) 
[Dec 14 2023, 4:12 PM]  block [289/1655] : done (7517ms) 
[Dec 14 2023, 4:12 PM]  block [290/1655] : done (7209ms) 
[Dec 14 2023, 4:12 PM]  block [291/1655] : done (7145ms) 
[Dec 14 2023, 4:12 PM]  block [292/1655] : done (7055ms) 
[Dec 14 2023, 4:12 PM]  block [293/1655] : done (6937ms) 
[Dec 14 2023, 4:12 PM]  block [294/1655] : done (7271ms) 
[Dec 14 2023, 4:12 PM]  block [295/1655] : done (7422ms) 
[Dec 14 2023, 4:12 PM]  block [296/1655] : done (7146ms) 
[Dec 14 2023, 4:13 PM]  block [297/1655] : done (7461ms) 
[Dec 14 2023, 4:13 PM]  block [298/1655] : done (7464ms) 
[Dec 14 2023, 4:13 PM]  block [299/1655] : done (7351ms) 
[Dec 14 2023, 4:13 PM]  block [300/1655] : done (6990ms) 
[Dec 14 2023, 4:13 PM]  block [301/1655] : done (7594ms) 
[Dec 14 2023, 4:13 PM] CPU: 31% (16 cores) * Memory: 12867/62826MB * Storage: 16/562GB * Net: 1↓/0↑MBps
[Dec 14 2023, 4:13 PM]  block [302/1655] : done (7353ms) 
[Dec 14 2023, 4:13 PM]  block [303/1655] : done (11487ms) 
[Dec 14 2023, 4:13 PM]  block [304/1655] : done (7793ms) 
[Dec 14 2023, 4:14 PM]  block [305/1655] : done (7320ms) 
[Dec 14 2023, 4:14 PM]  block [306/1655] : done (7183ms) 
[Dec 14 2023, 4:14 PM]  block [307/1655] : done (7543ms) 
[Dec 14 2023, 4:14 PM]  block [308/1655] : done (7333ms) 
[Dec 14 2023, 4:14 PM]  block [309/1655] : done (7042ms) 
[Dec 14 2023, 4:14 PM]  block [310/1655] : done (7214ms) 
[Dec 14 2023, 4:14 PM]  block [311/1655] : done (7454ms) 
[Dec 14 2023, 4:14 PM]  block [312/1655] : done (7185ms) 
[Dec 14 2023, 4:15 PM]  block [313/1655] : done (7406ms) 
[Dec 14 2023, 4:15 PM]  block [314/1655] : done (7438ms) 
[Dec 14 2023, 4:15 PM]  block [315/1655] : done (6932ms) 
[Dec 14 2023, 4:15 PM]  block [316/1655] : done (6953ms) 
[Dec 14 2023, 4:15 PM]  block [317/1655] : done (6878ms) 
[Dec 14 2023, 4:15 PM]  block [318/1655] : done (6991ms) 
[Dec 14 2023, 4:15 PM]  block [319/1655] : done (7399ms) 
[Dec 14 2023, 4:15 PM]  block [320/1655] : done (7435ms) 
[Dec 14 2023, 4:16 PM]  block [321/1655] : done (7478ms) 
[Dec 14 2023, 4:16 PM]  block [322/1655] : done (7914ms) 
[Dec 14 2023, 4:16 PM]  block [323/1655] : done (7966ms) 
[Dec 14 2023, 4:16 PM]  block [324/1655] : done (8033ms) 
[Dec 14 2023, 4:16 PM]  block [325/1655] : done (7494ms) 
[Dec 14 2023, 4:16 PM]  block [326/1655] : done (7812ms) 
[Dec 14 2023, 4:16 PM]  block [327/1655] : done (7986ms) 
[Dec 14 2023, 4:16 PM]  block [328/1655] : done (7441ms) 
[Dec 14 2023, 4:17 PM]  block [329/1655] : done (7477ms) 
[Dec 14 2023, 4:17 PM]  block [330/1655] : done (7326ms) 
[Dec 14 2023, 4:17 PM]  block [331/1655] : done (7362ms) 
[Dec 14 2023, 4:17 PM]  block [332/1655] : done (7562ms) 
[Dec 14 2023, 4:17 PM]  block [333/1655] : done (7538ms) 
[Dec 14 2023, 4:17 PM]  block [334/1655] : done (7614ms) 
[Dec 14 2023, 4:17 PM]  block [335/1655] : done (7724ms) 
[Dec 14 2023, 4:17 PM]  block [336/1655] : done (8135ms) 
[Dec 14 2023, 4:18 PM]  block [337/1655] : done (8794ms) 
[Dec 14 2023, 4:18 PM]  block [338/1655] : done (8295ms) 
[Dec 14 2023, 4:18 PM]  block [339/1655] : done (8472ms) 
[Dec 14 2023, 4:18 PM]  block [340/1655] : done (8017ms) 
[Dec 14 2023, 4:18 PM]  block [341/1655] : done (8175ms) 
[Dec 14 2023, 4:18 PM]  block [342/1655] : done (7993ms) 
[Dec 14 2023, 4:18 PM]  block [343/1655] : done (8025ms) 
[Dec 14 2023, 4:19 PM]  block [344/1655] : done (8690ms) 
[Dec 14 2023, 4:19 PM]  block [345/1655] : done (8055ms) 
[Dec 14 2023, 4:19 PM]  block [346/1655] : done (8523ms) 
[Dec 14 2023, 4:19 PM]  block [347/1655] : done (8768ms) 
[Dec 14 2023, 4:19 PM]  block [348/1655] : done (8122ms) 
[Dec 14 2023, 4:19 PM]  block [349/1655] : done (7946ms) 
[Dec 14 2023, 4:19 PM]  block [350/1655] : done (8247ms) 
[Dec 14 2023, 4:20 PM]  block [351/1655] : done (8131ms) 
[Dec 14 2023, 4:20 PM]  block [352/1655] : done (8568ms) 
[Dec 14 2023, 4:20 PM]  block [353/1655] : done (8481ms) 
[Dec 14 2023, 4:20 PM]  block [354/1655] : done (7900ms) 
[Dec 14 2023, 4:20 PM]  block [355/1655] : done (8017ms) 
[Dec 14 2023, 4:20 PM]  block [356/1655] : done (8114ms) 
[Dec 14 2023, 4:20 PM]  block [357/1655] : done (8108ms) 
[Dec 14 2023, 4:20 PM]  block [358/1655] : done (8115ms) 
[Dec 14 2023, 4:21 PM]  block [359/1655] : done (7884ms) 
[Dec 14 2023, 4:21 PM]  block [360/1655] : done (12756ms) 
[Dec 14 2023, 4:21 PM]  block [361/1655] : done (8088ms) 
[Dec 14 2023, 4:21 PM]  block [362/1655] : done (7983ms) 
[Dec 14 2023, 4:21 PM]  block [363/1655] : done (8263ms) 
[Dec 14 2023, 4:21 PM]  block [364/1655] : done (8058ms) 
[Dec 14 2023, 4:21 PM]  block [365/1655] : done (8273ms) 
[Dec 14 2023, 4:22 PM]  block [366/1655] : done (8816ms) 
[Dec 14 2023, 4:22 PM]  block [367/1655] : done (8721ms) 
[Dec 14 2023, 4:22 PM]  block [368/1655] : done (8858ms) 
[Dec 14 2023, 4:22 PM]  block [369/1655] : done (8144ms) 
[Dec 14 2023, 4:22 PM]  block [370/1655] : done (8055ms) 
[Dec 14 2023, 4:22 PM]  block [371/1655] : done (8375ms) 
[Dec 14 2023, 4:22 PM]  block [372/1655] : done (8264ms) 
[Dec 14 2023, 4:23 PM]  block [373/1655] : done (7720ms) 
[Dec 14 2023, 4:23 PM]  block [374/1655] : done (8048ms) 
[Dec 14 2023, 4:23 PM]  block [375/1655] : done (7903ms) 
[Dec 14 2023, 4:23 PM]  block [376/1655] : done (8194ms) 
[Dec 14 2023, 4:23 PM] CPU: 33% (16 cores) * Memory: 12015/62826MB * Storage: 16/562GB * Net: 1↓/0↑MBps
[Dec 14 2023, 4:23 PM]  block [377/1655] : done (7713ms) 
[Dec 14 2023, 4:23 PM]  block [378/1655] : done (7680ms) 
[Dec 14 2023, 4:23 PM]  block [379/1655] : done (7682ms) 
[Dec 14 2023, 4:24 PM]  block [380/1655] : done (7793ms) 
[Dec 14 2023, 4:24 PM]  block [381/1655] : done (7731ms) 
[Dec 14 2023, 4:24 PM]  block [382/1655] : done (8012ms) 
[Dec 14 2023, 4:24 PM]  block [383/1655] : done (7967ms) 
[Dec 14 2023, 4:24 PM]  block [384/1655] : done (7676ms) 
[Dec 14 2023, 4:24 PM]  block [385/1655] : done (7710ms) 
[Dec 14 2023, 4:24 PM]  block [386/1655] : done (8223ms) 
[Dec 14 2023, 4:24 PM]  block [387/1655] : done (7979ms) 
[Dec 14 2023, 4:25 PM]  block [388/1655] : done (8019ms) 
[Dec 14 2023, 4:25 PM]  block [389/1655] : done (7976ms) 
[Dec 14 2023, 4:25 PM]  block [390/1655] : done (8116ms) 
[Dec 14 2023, 4:25 PM]  block [391/1655] : done (8622ms) 
[Dec 14 2023, 4:25 PM]  block [392/1655] : done (7917ms) 
[Dec 14 2023, 4:25 PM]  block [393/1655] : done (7936ms) 
[Dec 14 2023, 4:25 PM]  block [394/1655] : done (8036ms) 
[Dec 14 2023, 4:26 PM]  block [395/1655] : done (8256ms) 
[Dec 14 2023, 4:26 PM]  block [396/1655] : done (8807ms) 
[Dec 14 2023, 4:26 PM]  block [397/1655] : done (8182ms) 
[Dec 14 2023, 4:26 PM]  block [398/1655] : done (8504ms) 
[Dec 14 2023, 4:26 PM]  block [399/1655] : done (12490ms) 
[Dec 14 2023, 4:26 PM]  block [400/1655] : done (8094ms) 
[Dec 14 2023, 4:26 PM]  block [401/1655] : done (8378ms) 
[Dec 14 2023, 4:27 PM]  block [402/1655] : done (8215ms) 
[Dec 14 2023, 4:27 PM]  block [403/1655] : done (9595ms) 
[Dec 14 2023, 4:27 PM]  block [404/1655] : done (8428ms) 
[Dec 14 2023, 4:27 PM]  block [405/1655] : done (8934ms) 
[Dec 14 2023, 4:27 PM]  block [406/1655] : done (8509ms) 
[Dec 14 2023, 4:27 PM]  block [407/1655] : done (8406ms) 
[Dec 14 2023, 4:27 PM]  block [408/1655] : done (8219ms) 
[Dec 14 2023, 4:28 PM]  block [409/1655] : done (8203ms) 
[Dec 14 2023, 4:28 PM]  block [410/1655] : done (8093ms) 
[Dec 14 2023, 4:28 PM]  block [411/1655] : done (8237ms) 
[Dec 14 2023, 4:28 PM]  block [412/1655] : done (7909ms) 
[Dec 14 2023, 4:28 PM]  block [413/1655] : done (7839ms) 
[Dec 14 2023, 4:28 PM]  block [414/1655] : done (12215ms) 
[Dec 14 2023, 4:28 PM]  block [415/1655] : done (7946ms) 
[Dec 14 2023, 4:29 PM]  block [416/1655] : done (8232ms) 
[Dec 14 2023, 4:29 PM]  block [417/1655] : done (8242ms) 
[Dec 14 2023, 4:29 PM]  block [418/1655] : done (8373ms) 
[Dec 14 2023, 4:29 PM]  block [419/1655] : done (8101ms) 
[Dec 14 2023, 4:29 PM]  block [420/1655] : done (7983ms) 
[Dec 14 2023, 4:29 PM]  block [421/1655] : done (7859ms) 
[Dec 14 2023, 4:29 PM]  block [422/1655] : done (8146ms) 
[Dec 14 2023, 4:30 PM]  block [423/1655] : done (8124ms) 
[Dec 14 2023, 4:30 PM]  block [424/1655] : done (8759ms) 
[Dec 14 2023, 4:30 PM]  block [425/1655] : done (8518ms) 
[Dec 14 2023, 4:30 PM]  block [426/1655] : done (8734ms) 
[Dec 14 2023, 4:30 PM]  block [427/1655] : done (8525ms) 
[Dec 14 2023, 4:30 PM]  block [428/1655] : done (8205ms) 
[Dec 14 2023, 4:30 PM]  block [429/1655] : done (8024ms) 
[Dec 14 2023, 4:31 PM]  block [430/1655] : done (8447ms) 
[Dec 14 2023, 4:31 PM]  block [431/1655] : done (8123ms) 
[Dec 14 2023, 4:31 PM]  block [432/1655] : done (8372ms) 
[Dec 14 2023, 4:31 PM]  block [433/1655] : done (8132ms) 
[Dec 14 2023, 4:31 PM]  block [434/1655] : done (8083ms) 
[Dec 14 2023, 4:31 PM]  block [435/1655] : done (8080ms) 
[Dec 14 2023, 4:31 PM]  block [436/1655] : done (7854ms) 
[Dec 14 2023, 4:31 PM]  block [437/1655] : done (9102ms) 
[Dec 14 2023, 4:32 PM]  block [438/1655] : done (8228ms) 
[Dec 14 2023, 4:32 PM]  block [439/1655] : done (8350ms) 
[Dec 14 2023, 4:32 PM]  block [440/1655] : done (8264ms) 
[Dec 14 2023, 4:32 PM]  block [441/1655] : done (8348ms) 
[Dec 14 2023, 4:32 PM]  block [442/1655] : done (8427ms) 
[Dec 14 2023, 4:32 PM]  block [443/1655] : done (8502ms) 
[Dec 14 2023, 4:32 PM]  block [444/1655] : done (8045ms) 
[Dec 14 2023, 4:33 PM]  block [445/1655] : done (9608ms) 
[Dec 14 2023, 4:33 PM]  block [446/1655] : done (7946ms) 
[Dec 14 2023, 4:33 PM]  block [447/1655] : done (8000ms) 
[Dec 14 2023, 4:33 PM]  block [448/1655] : done (8344ms) 
[Dec 14 2023, 4:33 PM] CPU: 34% (16 cores) * Memory: 11090/62826MB * Storage: 16/562GB * Net: 1↓/0↑MBps
[Dec 14 2023, 4:33 PM]  block [449/1655] : done (8019ms) 
[Dec 14 2023, 4:33 PM]  block [450/1655] : done (8161ms) 
[Dec 14 2023, 4:33 PM]  block [451/1655] : done (8819ms) 
[Dec 14 2023, 4:34 PM]  block [452/1655] : done (8596ms) 
[Dec 14 2023, 4:34 PM]  block [453/1655] : done (8402ms) 
[Dec 14 2023, 4:34 PM]  block [454/1655] : done (8512ms) 
[Dec 14 2023, 4:34 PM]  block [455/1655] : done (8866ms) 
[Dec 14 2023, 4:34 PM]  block [456/1655] : done (8913ms) 
[Dec 14 2023, 4:34 PM]  block [457/1655] : done (8585ms) 
[Dec 14 2023, 4:34 PM]  block [458/1655] : done (8057ms) 
[Dec 14 2023, 4:35 PM]  block [459/1655] : done (8776ms) 
[Dec 14 2023, 4:35 PM]  block [460/1655] : done (11441ms) 
[Dec 14 2023, 4:35 PM]  block [461/1655] : done (7973ms) 
[Dec 14 2023, 4:35 PM]  block [462/1655] : done (8169ms) 
[Dec 14 2023, 4:35 PM]  block [463/1655] : done (8189ms) 
[Dec 14 2023, 4:35 PM]  block [464/1655] : done (8318ms) 
[Dec 14 2023, 4:35 PM]  block [465/1655] : done (8172ms) 
[Dec 14 2023, 4:36 PM]  block [466/1655] : done (7846ms) 
[Dec 14 2023, 4:36 PM]  block [467/1655] : done (8214ms) 
[Dec 14 2023, 4:36 PM]  block [468/1655] : done (8340ms) 
[Dec 14 2023, 4:36 PM]  block [469/1655] : done (8256ms) 
[Dec 14 2023, 4:36 PM]  block [470/1655] : done (8119ms) 
[Dec 14 2023, 4:36 PM]  block [471/1655] : done (7915ms) 
[Dec 14 2023, 4:36 PM]  block [472/1655] : done (7918ms) 
[Dec 14 2023, 4:37 PM]  block [473/1655] : done (8481ms) 
[Dec 14 2023, 4:37 PM]  block [474/1655] : done (8356ms) 
[Dec 14 2023, 4:37 PM]  block [475/1655] : done (8049ms) 
[Dec 14 2023, 4:37 PM]  block [476/1655] : done (7949ms) 
[Dec 14 2023, 4:37 PM]  block [477/1655] : done (8397ms) 
[Dec 14 2023, 4:37 PM]  block [478/1655] : done (8481ms) 
[Dec 14 2023, 4:37 PM]  block [479/1655] : done (8192ms) 
[Dec 14 2023, 4:37 PM]  block [480/1655] : done (8224ms) 
[Dec 14 2023, 4:38 PM]  block [481/1655] : done (7973ms) 
[Dec 14 2023, 4:38 PM]  block [482/1655] : done (8861ms) 
[Dec 14 2023, 4:38 PM]  block [483/1655] : done (12791ms) 
[Dec 14 2023, 4:38 PM]  block [484/1655] : done (8214ms) 
[Dec 14 2023, 4:38 PM]  block [485/1655] : done (7928ms) 
[Dec 14 2023, 4:38 PM]  block [486/1655] : done (7740ms) 
[Dec 14 2023, 4:39 PM]  block [487/1655] : done (7740ms) 
[Dec 14 2023, 4:39 PM]  block [488/1655] : done (7777ms) 
[Dec 14 2023, 4:39 PM]  block [489/1655] : done (7746ms) 
[Dec 14 2023, 4:39 PM]  block [490/1655] : done (7830ms) 
[Dec 14 2023, 4:39 PM]  block [491/1655] : done (10442ms) 
[Dec 14 2023, 4:39 PM]  block [492/1655] : done (7878ms) 
[Dec 14 2023, 4:39 PM]  block [493/1655] : done (7734ms) 
[Dec 14 2023, 4:39 PM]  block [494/1655] : done (7985ms) 
[Dec 14 2023, 4:40 PM]  block [495/1655] : done (7681ms) 
[Dec 14 2023, 4:40 PM]  block [496/1655] : done (7813ms) 
[Dec 14 2023, 4:40 PM]  block [497/1655] : done (7941ms) 
[Dec 14 2023, 4:40 PM]  block [498/1655] : done (8086ms) 
[Dec 14 2023, 4:40 PM]  block [499/1655] : done (10044ms) 
[Dec 14 2023, 4:40 PM]  block [500/1655] : done (8018ms) 
[Dec 14 2023, 4:40 PM]  block [501/1655] : done (7957ms) 
[Dec 14 2023, 4:41 PM]  block [502/1655] : done (8202ms) 
[Dec 14 2023, 4:41 PM]  block [503/1655] : done (7872ms) 
[Dec 14 2023, 4:41 PM]  block [504/1655] : done (8280ms) 
[Dec 14 2023, 4:41 PM]  block [505/1655] : done (8404ms) 
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] +++ cat /home/dnanexus/meta/containerId
[Dec 14 2023, 4:41 PM] ++ docker wait 10d2b82317b5a8456fed368704e4f0a360b8f2704169e43797d133b26515c473
[Dec 14 2023, 4:41 PM] + rc=0
[Dec 14 2023, 4:41 PM] + exit 0
[Dec 14 2023, 4:41 PM] + rc=1
[Dec 14 2023, 4:41 PM] + [[ -f /home/dnanexus/meta/returnCode ]]
[Dec 14 2023, 4:41 PM] ++ cat /home/dnanexus/meta/returnCode
[Dec 14 2023, 4:41 PM] + file_rc=255
[Dec 14 2023, 4:41 PM] + [[ -z 255 ]]
[Dec 14 2023, 4:41 PM] + rc=255
[Dec 14 2023, 4:41 PM] + [[ 255 != 0 ]]
[Dec 14 2023, 4:41 PM] + [[ -f '' ]]
[Dec 14 2023, 4:41 PM] + exit 255
[Dec 14 2023, 4:41 PM]  block [506/1655] : 
[Dec 14 2023, 4:41 PM] [error] failure executing Task action 'run'
[Dec 14 2023, 4:41 PM] java.lang.Exception: job script function run_command exited with permanent fail code 255
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] PgrGet1() error 4
[Dec 14 2023, 4:41 PM] 
[Dec 14 2023, 4:41 PM]  at dx.executor.WorkerJobMeta.runJobScriptFunction(JobMeta.scala:987)
[Dec 14 2023, 4:41 PM]  at dx.executor.TaskExecutor.apply(TaskExecutor.scala:991)
[Dec 14 2023, 4:41 PM]  at dx.executor.BaseCli.dispatchCommand(BaseCli.scala:86)
[Dec 14 2023, 4:41 PM]  at dx.executor.BaseCli.main(BaseCli.scala:137)
[Dec 14 2023, 4:41 PM]  at dxExecutorWdl.MainApp$.delayedEndpoint$dxExecutorWdl$MainApp$1(Main.scala:27)
[Dec 14 2023, 4:41 PM]  at dxExecutorWdl.MainApp$delayedInit$body.apply(Main.scala:26)
[Dec 14 2023, 4:41 PM]  at scala.Function0.apply$mcV$sp(Function0.scala:39)
[Dec 14 2023, 4:41 PM]  at scala.Function0.apply$mcV$sp$(Function0.scala:39)
[Dec 14 2023, 4:41 PM]  at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
[Dec 14 2023, 4:41 PM]  at scala.App.$anonfun$main$1(App.scala:76)
[Dec 14 2023, 4:41 PM]  at scala.App.$anonfun$main$1$adapted(App.scala:76)
[Dec 14 2023, 4:41 PM]  at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563)
[Dec 14 2023, 4:41 PM]  at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561)
[Dec 14 2023, 4:41 PM]  at scala.collection.AbstractIterable.foreach(Iterable.scala:926)
[Dec 14 2023, 4:41 PM]  at scala.App.main(App.scala:76)
[Dec 14 2023, 4:41 PM]  at scala.App.main$(App.scala:74)
[Dec 14 2023, 4:41 PM]  at dxExecutorWdl.MainApp$.main(Main.scala:26)
[Dec 14 2023, 4:41 PM]  at dxExecutorWdl.MainApp.main(Main.scala)
[Dec 14 2023, 4:41 PM] 
[Dec 15 2023, 12:13 PM] END_LOG
joellembatchou commented 11 months ago

Hi,

This error comes from the plink libary, please check suggestion mentioned here: https://github.com/rgcgithub/regenie/issues/135#issuecomment-1856607237

Cheers, Joelle

joellembatchou commented 10 months ago

Are you streaming the files in the worfklow task or downloading them locally?

nikotzoumas commented 3 days ago

I had this issue with PLINK2.0 (.pgen) files on UK Biobank RAP, both using project paths and after downloading data locally. I got around it using BGEN and PLINK1.9 (.bed) format files.