Open prabhjyotsaini opened 1 year ago
I get this error:
INFO:root:log_message(***
Call: ./mixer.py fit1 \ --out /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.fit \ --lib /lustre03/project/6004655/COMMUN/soft/packages/mixer/src/build/lib/libbgmg.so \ --bim-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ --ld-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ --trait1-file /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz \ --extract /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps \ --threads 12 ) INFO:root:init(lib_name=/lustre03/project/6004655/COMMUN/soft/packages/mixer/src/build/lib/libbgmg.so, context_id=0) Traceback (most recent call last): File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer.py", line 23, in args.func(args) File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/cli.py", line 589, in execute_fit1_or_test1_parser results = init_results_struct(libbgmg, args) File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/cli.py", line 581, in init_results_struct results['options']['sum_weights'] = float(np.sum(libbgmg.weights)) File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/libbgmg.py", line 168, in weights return self._get_vec_impl(self.cdll.bgmg_retrieve_weights, np.float32, self.num_tag, trait=None) File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/libbgmg.py", line 410, in _get_vec_impl self._check_error(func(*args)) File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/libbgmg.py", line 418, in _check_error raise RuntimeError(self.get_last_error()) RuntimeError: runtime_error: arg <= 0
When I look in the log;
20230218 18:06:45.581056 ============= new session ============= 20230218 18:06:45.581929 = 20230218 18:06:45.581988 = mixer.py: Univariate and Bivariate Causal Mixture for GWAS 20230218 18:06:45.582042 = Version 1.2.0 20230218 18:06:45.582095 = (c) 2016-2020 Oleksandr Frei, Alexey A. Shadrin, Dominic Holland 20230218 18:06:45.582149 = Norwegian Centre for Mental Disorders Research / University of Oslo 20230218 18:06:45.582203 = Center for Multimodal Imaging and Genetics / UCSD 20230218 18:06:45.582256 = GNU General Public License v3 20230218 18:06:45.582310 = 20230218 18:06:45.582363 =Call: 20230218 18:06:45.582417 =./mixer.py fit1 \ 20230218 18:06:45.582470 = --out /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.fit \ 20230218 18:06:45.582524 = --lib /lustre03/project/6004655/COMMUN/soft/packages/mixer/src/build/lib/libbgmg.so \ 20230218 18:06:45.582577 = --bim-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ 20230218 18:06:45.582631 = --ld-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ 20230218 18:06:45.582684 = --trait1-file /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz \ 20230218 18:06:45.582738 = --extract /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps \ 20230218 18:06:45.582791 = --threads 12 20230218 18:06:45.582879 Dispose context (id=0) 20230218 18:06:45.584348 Create new context (id=0) 20230218 18:06:45.584453 >init(bim_file=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim, frq_file=, chr_labels=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22, trait1_file=/home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz, trait2_file=, exclude=, extract=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps); 20230218 18:06:45.585120 Construct reference from 22 files... 20230218 18:06:46.239377 Found 438106 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.bim 20230218 18:06:46.326204 Found 480110 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.bim 20230218 18:06:46.342061 Found 493922 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.bim 20230218 18:06:46.364627 Found 510501 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.bim 20230218 18:06:46.461833 Found 549971 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.bim 20230218 18:06:46.529707 Found 589569 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.bim 20230218 18:06:46.578410 Found 633015 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.bim 20230218 18:06:46.628609 Found 664016 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.bim 20230218 18:06:46.681756 Found 706350 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.bim 20230218 18:06:46.713324 Found 729645 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.bim 20230218 18:06:46.783418 Found 779354 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.bim 20230218 18:06:46.804751 Found 287001 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.bim 20230218 18:06:46.807536 Found 366200 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.bim 20230218 18:06:46.833264 Found 324698 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.bim 20230218 18:06:46.858296 Found 316981 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.bim 20230218 18:06:46.871886 Found 839590 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.bim 20230218 18:06:46.879550 Found 269222 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.bim 20230218 18:06:46.899217 Found 138712 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.bim 20230218 18:06:46.926255 Found 232363 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.bim 20230218 18:06:46.933985 Found 141123 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.bim 20230218 18:06:46.962180 Found 285156 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.bim 20230218 18:06:46.963440 Found 221626 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.bim 20230218 18:06:47.444536 Found 9997231 variants in total. 20230218 18:09:05.525631 Found 6564637 variants with well-defined Z and N in /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz. Other statistics: 20230218 18:09:05.570104 8130258 lines found (including header) 20230218 18:09:05.570171 7445470 lines matched via CHR:BP:A1:A2 code (not SNP rs#) 20230218 18:09:05.570236 684787 lines were ignored as RS# (or chr:bp:a1:a2 code) did not match reference file. 20230218 18:09:05.570300 880833 variants were ignored as they are strand-ambiguous. 20230218 18:09:05.570364 5259074 variants had flipped A1/A2 alleles; sign of z-score was flipped. 20230218 18:09:05.581781 constrain analysis to 6564637 tag variants (due to trait1_file='/home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz') 20230218 18:09:08.297440 constrain analysis to 0 tag variants (due to extract='/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps') 20230218 18:09:08.321756 set_tag_indices(num_snp=9997231, num_tag=0); 20230218 18:09:08.342960 >set_chrnumvec(9997231); 20230218 18:09:08.359099 <set_chrnumvec(9997231); 20230218 18:09:08.359225 >LdMatrixCsr::init_chunks(); 20230218 18:09:08.500125 highest chr label: 22 20230218 18:09:08.571230 <LdMatrixCsr::init_chunks(); 20230218 18:09:08.571300 set_zvec(trait=1); num_undef=0 20230218 18:09:08.571374 set_nvec(trait=1); num_undef=0 20230218 18:09:08.571448 <init(bim_file=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim, frq_file=, chr_labels=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22, trait1_file=/home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz, trait2_file=, exclude=, extract=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps); elapsed time 142986ms 20230218 18:09:08.573155 set_option(r2min=0); 20230218 18:09:08.573566 set_option(kmax=20000); 20230218 18:09:08.573664 clear_state 20230218 18:09:08.573753 set_option(threads=12); 20230218 18:09:08.573853 omp_set_num_threads(12) 20230218 18:09:08.573949 set_option(seed=123); 20230218 18:09:08.574072 set_option(cubature_rel_error=1e-05); 20230218 18:09:08.574175 set_option(cubature_max_evals=1000); 20230218 18:09:08.574329 initialize mafvec 20230218 18:09:08.585094 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld) 20230218 18:09:08.791160 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld), format version 1 20230218 18:09:08.791304 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld, numel=142187412)... 20230218 18:09:10.572193 >set_ld_r2_coo(chr_label=1, length=142187412); 20230218 18:09:10.942778 LdMatrixCsr::init_diagonal(chr_label=1) added 0 tag (out of 779354 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:09:20.625522 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 9697 ms 20230218 18:09:20.634908 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.run4.ld) 20230218 18:09:20.868092 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.run4.ld), format version 1 20230218 18:09:20.868229 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.run4.ld, numel=168279433)... 20230218 18:09:23.018676 >set_ld_r2_coo(chr_label=2, length=168279433); 20230218 18:09:23.473882 LdMatrixCsr::init_diagonal(chr_label=2) added 0 tag (out of 839590 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:09:34.895063 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 11433 ms 20230218 18:09:34.903580 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.run4.ld) 20230218 18:09:35.119299 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.run4.ld), format version 1 20230218 18:09:35.119437 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.run4.ld, numel=152994339)... 20230218 18:09:37.019741 >set_ld_r2_coo(chr_label=3, length=152994339); 20230218 18:09:37.416992 LdMatrixCsr::init_diagonal(chr_label=3) added 0 tag (out of 706350 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:09:47.764181 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 10357 ms 20230218 18:09:47.770766 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.run4.ld) 20230218 18:09:47.992476 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.run4.ld), format version 1 20230218 18:09:47.992614 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.run4.ld, numel=160729596)... 20230218 18:09:49.977533 >set_ld_r2_coo(chr_label=4, length=160729596); 20230218 18:09:50.393391 LdMatrixCsr::init_diagonal(chr_label=4) added 0 tag (out of 729645 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:01.288577 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 10905 ms 20230218 18:10:01.295487 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.run4.ld) 20230218 18:10:01.492432 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.run4.ld), format version 1 20230218 18:10:01.492569 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.run4.ld, numel=136099527)... 20230218 18:10:03.184601 >set_ld_r2_coo(chr_label=5, length=136099527); 20230218 18:10:03.537911 LdMatrixCsr::init_diagonal(chr_label=5) added 0 tag (out of 633015 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:12.732614 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 9203 ms 20230218 18:10:12.738675 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.run4.ld) 20230218 18:10:13.046782 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.run4.ld), format version 1 20230218 18:10:13.046933 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.run4.ld, numel=228187530)... 20230218 18:10:15.874086 >set_ld_r2_coo(chr_label=6, length=228187530); 20230218 18:10:16.462471 LdMatrixCsr::init_diagonal(chr_label=6) added 0 tag (out of 664016 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:31.806513 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 15352 ms 20230218 18:10:31.818144 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.run4.ld) 20230218 18:10:31.998450 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.run4.ld), format version 1 20230218 18:10:31.998585 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.run4.ld, numel=126547337)... 20230218 18:10:33.578516 >set_ld_r2_coo(chr_label=7, length=126547337); 20230218 18:10:33.905628 LdMatrixCsr::init_diagonal(chr_label=7) added 0 tag (out of 589569 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:42.502567 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 8605 ms 20230218 18:10:42.508545 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.run4.ld) 20230218 18:10:42.695768 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.run4.ld), format version 1 20230218 18:10:42.695920 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.run4.ld, numel=136913989)... 20230218 18:10:44.394053 >set_ld_r2_coo(chr_label=8, length=136913989); 20230218 18:10:44.747704 LdMatrixCsr::init_diagonal(chr_label=8) added 0 tag (out of 549971 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:53.989694 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 9250 ms 20230218 18:10:53.997074 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.run4.ld) 20230218 18:10:54.112737 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.run4.ld), format version 1 20230218 18:10:54.113023 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.run4.ld, numel=77579006)... 20230218 18:10:55.096129 >set_ld_r2_coo(chr_label=9, length=77579006); 20230218 18:10:55.299862 LdMatrixCsr::init_diagonal(chr_label=9) added 0 tag (out of 438106 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:00.568003 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 5274 ms 20230218 18:11:00.572381 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.run4.ld) 20230218 18:11:00.738038 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.run4.ld), format version 1 20230218 18:11:00.738180 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.run4.ld, numel=119085534)... 20230218 18:11:02.215275 >set_ld_r2_coo(chr_label=10, length=119085534); 20230218 18:11:02.524065 LdMatrixCsr::init_diagonal(chr_label=10) added 0 tag (out of 510501 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:10.567710 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 8054 ms 20230218 18:11:10.577774 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.run4.ld) 20230218 18:11:10.832451 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.run4.ld), format version 1 20230218 18:11:10.832588 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.run4.ld, numel=188824128)... 20230218 18:11:13.131916 >set_ld_r2_coo(chr_label=11, length=188824128); 20230218 18:11:13.616850 LdMatrixCsr::init_diagonal(chr_label=11) added 0 tag (out of 493922 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:26.270938 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 12661 ms 20230218 18:11:26.278650 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.run4.ld) 20230218 18:11:26.433771 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.run4.ld), format version 1 20230218 18:11:26.433923 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.run4.ld, numel=109885217)... 20230218 18:11:27.811796 >set_ld_r2_coo(chr_label=12, length=109885217); 20230218 18:11:28.095953 LdMatrixCsr::init_diagonal(chr_label=12) added 0 tag (out of 480110 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:35.549984 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 7461 ms 20230218 18:11:35.555177 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.run4.ld) 20230218 18:11:35.657415 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.run4.ld), format version 1 20230218 18:11:35.657584 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.run4.ld, numel=70960188)... 20230218 18:11:36.552507 >set_ld_r2_coo(chr_label=13, length=70960188); 20230218 18:11:36.737109 LdMatrixCsr::init_diagonal(chr_label=13) added 0 tag (out of 366200 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:41.558440 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 4826 ms 20230218 18:11:41.562480 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.run4.ld) 20230218 18:11:41.652146 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.run4.ld), format version 1 20230218 18:11:41.652284 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.run4.ld, numel=63040380)... 20230218 18:11:42.448485 >set_ld_r2_coo(chr_label=14, length=63040380); 20230218 18:11:42.613304 LdMatrixCsr::init_diagonal(chr_label=14) added 0 tag (out of 324698 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:46.889224 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 4280 ms 20230218 18:11:46.894241 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.run4.ld) 20230218 18:11:46.969253 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.run4.ld), format version 1 20230218 18:11:46.969388 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.run4.ld, numel=49926090)... 20230218 18:11:47.605484 >set_ld_r2_coo(chr_label=15, length=49926090); 20230218 18:11:47.737150 LdMatrixCsr::init_diagonal(chr_label=15) added 0 tag (out of 287001 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:51.133444 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3400 ms 20230218 18:11:51.136648 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.run4.ld) 20230218 18:11:51.211359 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.run4.ld), format version 1 20230218 18:11:51.211495 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.run4.ld, numel=50134831)... 20230218 18:11:51.858708 >set_ld_r2_coo(chr_label=16, length=50134831); 20230218 18:11:51.996136 LdMatrixCsr::init_diagonal(chr_label=16) added 0 tag (out of 316981 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:55.424594 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3433 ms 20230218 18:11:55.427904 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.run4.ld) 20230218 18:11:55.490568 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.run4.ld), format version 1 20230218 18:11:55.490705 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.run4.ld, numel=44545217)... 20230218 18:11:56.056812 >set_ld_r2_coo(chr_label=17, length=44545217); 20230218 18:11:56.175631 LdMatrixCsr::init_diagonal(chr_label=17) added 0 tag (out of 269222 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:59.217779 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3046 ms 20230218 18:11:59.220646 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.run4.ld) 20230218 18:11:59.288375 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.run4.ld), format version 1 20230218 18:11:59.288515 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.run4.ld, numel=46210988)... 20230218 18:11:59.880118 >set_ld_r2_coo(chr_label=18, length=46210988); 20230218 18:12:00.001560 LdMatrixCsr::init_diagonal(chr_label=18) added 0 tag (out of 285156 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:03.154276 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3157 ms 20230218 18:12:03.158564 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.run4.ld) 20230218 18:12:03.222390 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.run4.ld), format version 1 20230218 18:12:03.222527 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.run4.ld, numel=41832078)... 20230218 18:12:03.755643 >set_ld_r2_coo(chr_label=19, length=41832078); 20230218 18:12:03.865060 LdMatrixCsr::init_diagonal(chr_label=19) added 0 tag (out of 232363 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:06.716486 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 2854 ms 20230218 18:12:06.719090 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.run4.ld) 20230218 18:12:06.763842 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.run4.ld), format version 1 20230218 18:12:06.763982 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.run4.ld, numel=32520107)... 20230218 18:12:07.182275 >set_ld_r2_coo(chr_label=20, length=32520107); 20230218 18:12:07.267073 LdMatrixCsr::init_diagonal(chr_label=20) added 0 tag (out of 221626 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:09.474914 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 2210 ms 20230218 18:12:09.477185 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.run4.ld) 20230218 18:12:09.503141 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.run4.ld), format version 1 20230218 18:12:09.503280 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.run4.ld, numel=19431920)... 20230218 18:12:09.755649 >set_ld_r2_coo(chr_label=21, length=19431920); 20230218 18:12:09.806819 LdMatrixCsr::init_diagonal(chr_label=21) added 0 tag (out of 138712 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:11.126975 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 1322 ms 20230218 18:12:11.128899 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.run4.ld) 20230218 18:12:11.154638 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.run4.ld), format version 1 20230218 18:12:11.154774 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.run4.ld, numel=19295890)... 20230218 18:12:11.407822 >set_ld_r2_coo(chr_label=22, length=19295890); 20230218 18:12:11.459199 LdMatrixCsr::init_diagonal(chr_label=22) added 0 tag (out of 141123 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:12.764309 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 1307 ms 20230218 18:12:12.766229 >set_weights_randprune(n=64, r2=0.1, exclude=, extract=) 20230218 18:12:12.777641 <set_weights_randprune(n=64, r2=0.1, exclude=, extract=), elapsed time 11ms 20230218 18:12:12.778243 set_option(diag=0); 20230218 18:12:12.778351 diag: numsnp=9997231 20230218 18:12:12.778406 diag: numtag=0 20230218 18:12:12.778460 diag: LdMatrixCsr 23 chunks in total. Logging futher info for non-empty chunks only. 20230218 18:12:12.778524 diag: zvec1.size()=0 20230218 18:12:12.778578 diag: zvec1=[], nnz=0 20230218 18:12:12.778634 diag: nvec1.size()=0 20230218 18:12:12.778688 diag: nvec1=[], nnz=0 20230218 18:12:12.778743 diag: causalbetavec1.size()=0 20230218 18:12:12.778797 diag: causalbetavec1=[], nnz=0 20230218 18:12:12.778861 diag: zvec2.size()=0 20230218 18:12:12.778935 diag: zvec2=[], nnz=0 20230218 18:12:12.778991 diag: nvec2.size()=0 20230218 18:12:12.779044 diag: nvec2=[], nnz=0 20230218 18:12:12.779099 diag: causalbetavec2.size()=0 20230218 18:12:12.779153 diag: causalbetavec2=[], nnz=0 20230218 18:12:12.779208 diag: weights.size()=0 20230218 18:12:12.779261 diag: weights=[], nnz=0 20230218 18:12:12.779316 diag: mafvec.size()=9997231 20230218 18:12:12.779370 diag: mafvec=[0.911043, 0.911043, 0.945808, 0.811861, 0.811861, ...], nnz=9997231 20230218 18:12:12.792650 diag: options.kmax=20000 20230218 18:12:12.792710 diag: options.use_complete_tagindices=0 20230218 18:12:12.792769 diag: options.disable_snp_to_tagmap=0 20230218 18:12:12.792830 diag: options.maxcausals=100000 20230218 18:12:12.792884 diag: options.numcomponents=1 20230218 18:12:12.792937 diag: options.r2min=0 20230218 18:12:12.792995 diag: options.z1max=1e+10 20230218 18:12:12.793051 diag: options.z2max=1e+10 20230218 18:12:12.793107 diag: options.costcalculator=0 (Sampling) 20230218 18:12:12.793171 diag: options.auxoption=1 (Ezvec2) 20230218 18:12:12.793234 diag: options.cache_tagr2sum=no 20230218 18:12:12.793287 diag: options.seed_=123 20230218 18:12:12.793341 diag: options.cubature_abserror=0 20230218 18:12:12.793396 diag: options.cubature_relerror=1e-05 20230218 18:12:12.793452 diag: options.cubature_maxevals=1000 20230218 18:12:12.793506 diag: options.calc_kpdf=0 20230218 18:12:12.793559 diag: options.ld_formatversion=-1 20230218 18:12:12.793613 diag: options.retrieve_ld_sumtype=0 20230218 18:12:12.793666 diag: Estimated memory usage (total): 0 bytes 20230218 18:12:12.794132 retrieve_mafvec() 20230218 18:12:12.806116 retrieve_mafvec() 20230218 18:12:12.837644 runtime_error: arg <= 0
I tried this using the SCZ data that was included.
I get this error:
INFO:root:log_message(***
Call: ./mixer.py fit1 \ --out /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.fit \ --lib /lustre03/project/6004655/COMMUN/soft/packages/mixer/src/build/lib/libbgmg.so \ --bim-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ --ld-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ --trait1-file /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz \ --extract /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps \ --threads 12 ) INFO:root:init(lib_name=/lustre03/project/6004655/COMMUN/soft/packages/mixer/src/build/lib/libbgmg.so, context_id=0) Traceback (most recent call last): File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer.py", line 23, in
args.func(args)
File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/cli.py", line 589, in execute_fit1_or_test1_parser
results = init_results_struct(libbgmg, args)
File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/cli.py", line 581, in init_results_struct
results['options']['sum_weights'] = float(np.sum(libbgmg.weights))
File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/libbgmg.py", line 168, in weights
return self._get_vec_impl(self.cdll.bgmg_retrieve_weights, np.float32, self.num_tag, trait=None)
File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/libbgmg.py", line 410, in _get_vec_impl
self._check_error(func(*args))
File "/lustre03/project/6004655/COMMUN/soft/packages/mixer/precimed/mixer/libbgmg.py", line 418, in _check_error
raise RuntimeError(self.get_last_error())
RuntimeError: runtime_error: arg <= 0
When I look in the log;
20230218 18:06:45.581056 ============= new session ============= 20230218 18:06:45.581929 = 20230218 18:06:45.581988 = mixer.py: Univariate and Bivariate Causal Mixture for GWAS 20230218 18:06:45.582042 = Version 1.2.0 20230218 18:06:45.582095 = (c) 2016-2020 Oleksandr Frei, Alexey A. Shadrin, Dominic Holland 20230218 18:06:45.582149 = Norwegian Centre for Mental Disorders Research / University of Oslo 20230218 18:06:45.582203 = Center for Multimodal Imaging and Genetics / UCSD 20230218 18:06:45.582256 = GNU General Public License v3 20230218 18:06:45.582310 = 20230218 18:06:45.582363 =Call: 20230218 18:06:45.582417 =./mixer.py fit1 \ 20230218 18:06:45.582470 = --out /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.fit \ 20230218 18:06:45.582524 = --lib /lustre03/project/6004655/COMMUN/soft/packages/mixer/src/build/lib/libbgmg.so \ 20230218 18:06:45.582577 = --bim-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ 20230218 18:06:45.582631 = --ld-file /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ 20230218 18:06:45.582684 = --trait1-file /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz \ 20230218 18:06:45.582738 = --extract /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps \ 20230218 18:06:45.582791 = --threads 12 20230218 18:06:45.582879 Dispose context (id=0) 20230218 18:06:45.584348 Create new context (id=0) 20230218 18:06:45.584453 >init(bim_file=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim, frq_file=, chr_labels=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22, trait1_file=/home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz, trait2_file=, exclude=, extract=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps); 20230218 18:06:45.585120 Construct reference from 22 files... 20230218 18:06:46.239377 Found 438106 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.bim 20230218 18:06:46.326204 Found 480110 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.bim 20230218 18:06:46.342061 Found 493922 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.bim 20230218 18:06:46.364627 Found 510501 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.bim 20230218 18:06:46.461833 Found 549971 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.bim 20230218 18:06:46.529707 Found 589569 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.bim 20230218 18:06:46.578410 Found 633015 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.bim 20230218 18:06:46.628609 Found 664016 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.bim 20230218 18:06:46.681756 Found 706350 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.bim 20230218 18:06:46.713324 Found 729645 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.bim 20230218 18:06:46.783418 Found 779354 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.bim 20230218 18:06:46.804751 Found 287001 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.bim 20230218 18:06:46.807536 Found 366200 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.bim 20230218 18:06:46.833264 Found 324698 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.bim 20230218 18:06:46.858296 Found 316981 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.bim 20230218 18:06:46.871886 Found 839590 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.bim 20230218 18:06:46.879550 Found 269222 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.bim 20230218 18:06:46.899217 Found 138712 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.bim 20230218 18:06:46.926255 Found 232363 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.bim 20230218 18:06:46.933985 Found 141123 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.bim 20230218 18:06:46.962180 Found 285156 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.bim 20230218 18:06:46.963440 Found 221626 variants in /lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.bim 20230218 18:06:47.444536 Found 9997231 variants in total. 20230218 18:09:05.525631 Found 6564637 variants with well-defined Z and N in /home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz. Other statistics: 20230218 18:09:05.570104 8130258 lines found (including header) 20230218 18:09:05.570171 7445470 lines matched via CHR:BP:A1:A2 code (not SNP rs#) 20230218 18:09:05.570236 684787 lines were ignored as RS# (or chr:bp:a1:a2 code) did not match reference file. 20230218 18:09:05.570300 880833 variants were ignored as they are strand-ambiguous. 20230218 18:09:05.570364 5259074 variants had flipped A1/A2 alleles; sign of z-score was flipped. 20230218 18:09:05.581781 constrain analysis to 6564637 tag variants (due to trait1_file='/home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz') 20230218 18:09:08.297440 constrain analysis to 0 tag variants (due to extract='/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps') 20230218 18:09:08.321756 set_tag_indices(num_snp=9997231, num_tag=0); 20230218 18:09:08.342960 >set_chrnumvec(9997231); 20230218 18:09:08.359099 <set_chrnumvec(9997231); 20230218 18:09:08.359225 >LdMatrixCsr::init_chunks(); 20230218 18:09:08.500125 highest chr label: 22 20230218 18:09:08.571230 <LdMatrixCsr::init_chunks(); 20230218 18:09:08.571300 set_zvec(trait=1); num_undef=0 20230218 18:09:08.571374 set_nvec(trait=1); num_undef=0 20230218 18:09:08.571448 <init(bim_file=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim, frq_file=, chr_labels=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22, trait1_file=/home/psaini/scratch/ProjectFolder_CombinedGWAS/Applications/SCZ.sumstats.gz, trait2_file=, exclude=, extract=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.snps); elapsed time 142986ms 20230218 18:09:08.573155 set_option(r2min=0); 20230218 18:09:08.573566 set_option(kmax=20000); 20230218 18:09:08.573664 clear_state 20230218 18:09:08.573753 set_option(threads=12); 20230218 18:09:08.573853 omp_set_num_threads(12) 20230218 18:09:08.573949 set_option(seed=123); 20230218 18:09:08.574072 set_option(cubature_rel_error=1e-05); 20230218 18:09:08.574175 set_option(cubature_max_evals=1000); 20230218 18:09:08.574329 initialize mafvec 20230218 18:09:08.585094 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld) 20230218 18:09:08.791160 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld), format version 1 20230218 18:09:08.791304 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.run4.ld, numel=142187412)... 20230218 18:09:10.572193 >set_ld_r2_coo(chr_label=1, length=142187412); 20230218 18:09:10.942778 LdMatrixCsr::init_diagonal(chr_label=1) added 0 tag (out of 779354 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:09:20.625522 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 9697 ms 20230218 18:09:20.634908 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.run4.ld) 20230218 18:09:20.868092 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.run4.ld), format version 1 20230218 18:09:20.868229 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.run4.ld, numel=168279433)... 20230218 18:09:23.018676 >set_ld_r2_coo(chr_label=2, length=168279433); 20230218 18:09:23.473882 LdMatrixCsr::init_diagonal(chr_label=2) added 0 tag (out of 839590 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:09:34.895063 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 11433 ms 20230218 18:09:34.903580 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.run4.ld) 20230218 18:09:35.119299 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.run4.ld), format version 1 20230218 18:09:35.119437 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.run4.ld, numel=152994339)... 20230218 18:09:37.019741 >set_ld_r2_coo(chr_label=3, length=152994339); 20230218 18:09:37.416992 LdMatrixCsr::init_diagonal(chr_label=3) added 0 tag (out of 706350 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:09:47.764181 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 10357 ms 20230218 18:09:47.770766 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.run4.ld) 20230218 18:09:47.992476 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.run4.ld), format version 1 20230218 18:09:47.992614 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.run4.ld, numel=160729596)... 20230218 18:09:49.977533 >set_ld_r2_coo(chr_label=4, length=160729596); 20230218 18:09:50.393391 LdMatrixCsr::init_diagonal(chr_label=4) added 0 tag (out of 729645 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:01.288577 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 10905 ms 20230218 18:10:01.295487 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.run4.ld) 20230218 18:10:01.492432 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.run4.ld), format version 1 20230218 18:10:01.492569 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.run4.ld, numel=136099527)... 20230218 18:10:03.184601 >set_ld_r2_coo(chr_label=5, length=136099527); 20230218 18:10:03.537911 LdMatrixCsr::init_diagonal(chr_label=5) added 0 tag (out of 633015 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:12.732614 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 9203 ms 20230218 18:10:12.738675 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.run4.ld) 20230218 18:10:13.046782 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.run4.ld), format version 1 20230218 18:10:13.046933 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.run4.ld, numel=228187530)... 20230218 18:10:15.874086 >set_ld_r2_coo(chr_label=6, length=228187530); 20230218 18:10:16.462471 LdMatrixCsr::init_diagonal(chr_label=6) added 0 tag (out of 664016 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:31.806513 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 15352 ms 20230218 18:10:31.818144 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.run4.ld) 20230218 18:10:31.998450 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.run4.ld), format version 1 20230218 18:10:31.998585 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.run4.ld, numel=126547337)... 20230218 18:10:33.578516 >set_ld_r2_coo(chr_label=7, length=126547337); 20230218 18:10:33.905628 LdMatrixCsr::init_diagonal(chr_label=7) added 0 tag (out of 589569 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:42.502567 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 8605 ms 20230218 18:10:42.508545 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.run4.ld) 20230218 18:10:42.695768 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.run4.ld), format version 1 20230218 18:10:42.695920 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.8.run4.ld, numel=136913989)... 20230218 18:10:44.394053 >set_ld_r2_coo(chr_label=8, length=136913989); 20230218 18:10:44.747704 LdMatrixCsr::init_diagonal(chr_label=8) added 0 tag (out of 549971 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:10:53.989694 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 9250 ms 20230218 18:10:53.997074 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.run4.ld) 20230218 18:10:54.112737 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.run4.ld), format version 1 20230218 18:10:54.113023 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.run4.ld, numel=77579006)... 20230218 18:10:55.096129 >set_ld_r2_coo(chr_label=9, length=77579006); 20230218 18:10:55.299862 LdMatrixCsr::init_diagonal(chr_label=9) added 0 tag (out of 438106 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:00.568003 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 5274 ms 20230218 18:11:00.572381 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.run4.ld) 20230218 18:11:00.738038 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.run4.ld), format version 1 20230218 18:11:00.738180 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.10.run4.ld, numel=119085534)... 20230218 18:11:02.215275 >set_ld_r2_coo(chr_label=10, length=119085534); 20230218 18:11:02.524065 LdMatrixCsr::init_diagonal(chr_label=10) added 0 tag (out of 510501 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:10.567710 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 8054 ms 20230218 18:11:10.577774 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.run4.ld) 20230218 18:11:10.832451 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.run4.ld), format version 1 20230218 18:11:10.832588 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.run4.ld, numel=188824128)... 20230218 18:11:13.131916 >set_ld_r2_coo(chr_label=11, length=188824128); 20230218 18:11:13.616850 LdMatrixCsr::init_diagonal(chr_label=11) added 0 tag (out of 493922 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:26.270938 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 12661 ms 20230218 18:11:26.278650 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.run4.ld) 20230218 18:11:26.433771 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.run4.ld), format version 1 20230218 18:11:26.433923 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.12.run4.ld, numel=109885217)... 20230218 18:11:27.811796 >set_ld_r2_coo(chr_label=12, length=109885217); 20230218 18:11:28.095953 LdMatrixCsr::init_diagonal(chr_label=12) added 0 tag (out of 480110 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:35.549984 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 7461 ms 20230218 18:11:35.555177 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.run4.ld) 20230218 18:11:35.657415 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.run4.ld), format version 1 20230218 18:11:35.657584 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.13.run4.ld, numel=70960188)... 20230218 18:11:36.552507 >set_ld_r2_coo(chr_label=13, length=70960188); 20230218 18:11:36.737109 LdMatrixCsr::init_diagonal(chr_label=13) added 0 tag (out of 366200 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:41.558440 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 4826 ms 20230218 18:11:41.562480 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.run4.ld) 20230218 18:11:41.652146 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.run4.ld), format version 1 20230218 18:11:41.652284 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.14.run4.ld, numel=63040380)... 20230218 18:11:42.448485 >set_ld_r2_coo(chr_label=14, length=63040380); 20230218 18:11:42.613304 LdMatrixCsr::init_diagonal(chr_label=14) added 0 tag (out of 324698 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:46.889224 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 4280 ms 20230218 18:11:46.894241 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.run4.ld) 20230218 18:11:46.969253 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.run4.ld), format version 1 20230218 18:11:46.969388 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.15.run4.ld, numel=49926090)... 20230218 18:11:47.605484 >set_ld_r2_coo(chr_label=15, length=49926090); 20230218 18:11:47.737150 LdMatrixCsr::init_diagonal(chr_label=15) added 0 tag (out of 287001 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:51.133444 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3400 ms 20230218 18:11:51.136648 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.run4.ld) 20230218 18:11:51.211359 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.run4.ld), format version 1 20230218 18:11:51.211495 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.run4.ld, numel=50134831)... 20230218 18:11:51.858708 >set_ld_r2_coo(chr_label=16, length=50134831); 20230218 18:11:51.996136 LdMatrixCsr::init_diagonal(chr_label=16) added 0 tag (out of 316981 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:55.424594 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3433 ms 20230218 18:11:55.427904 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.run4.ld) 20230218 18:11:55.490568 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.run4.ld), format version 1 20230218 18:11:55.490705 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.run4.ld, numel=44545217)... 20230218 18:11:56.056812 >set_ld_r2_coo(chr_label=17, length=44545217); 20230218 18:11:56.175631 LdMatrixCsr::init_diagonal(chr_label=17) added 0 tag (out of 269222 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:11:59.217779 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3046 ms 20230218 18:11:59.220646 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.run4.ld) 20230218 18:11:59.288375 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.run4.ld), format version 1 20230218 18:11:59.288515 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.run4.ld, numel=46210988)... 20230218 18:11:59.880118 >set_ld_r2_coo(chr_label=18, length=46210988); 20230218 18:12:00.001560 LdMatrixCsr::init_diagonal(chr_label=18) added 0 tag (out of 285156 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:03.154276 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 3157 ms 20230218 18:12:03.158564 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.run4.ld) 20230218 18:12:03.222390 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.run4.ld), format version 1 20230218 18:12:03.222527 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.run4.ld, numel=41832078)... 20230218 18:12:03.755643 >set_ld_r2_coo(chr_label=19, length=41832078); 20230218 18:12:03.865060 LdMatrixCsr::init_diagonal(chr_label=19) added 0 tag (out of 232363 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:06.716486 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 2854 ms 20230218 18:12:06.719090 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.run4.ld) 20230218 18:12:06.763842 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.run4.ld), format version 1 20230218 18:12:06.763982 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.run4.ld, numel=32520107)... 20230218 18:12:07.182275 >set_ld_r2_coo(chr_label=20, length=32520107); 20230218 18:12:07.267073 LdMatrixCsr::init_diagonal(chr_label=20) added 0 tag (out of 221626 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:09.474914 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 2210 ms 20230218 18:12:09.477185 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.run4.ld) 20230218 18:12:09.503141 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.run4.ld), format version 1 20230218 18:12:09.503280 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.run4.ld, numel=19431920)... 20230218 18:12:09.755649 >set_ld_r2_coo(chr_label=21, length=19431920); 20230218 18:12:09.806819 LdMatrixCsr::init_diagonal(chr_label=21) added 0 tag (out of 138712 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:11.126975 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 1322 ms 20230218 18:12:11.128899 >load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.run4.ld) 20230218 18:12:11.154638 <load_ld_matrix(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.run4.ld), format version 1 20230218 18:12:11.154774 set_ld_r2_coo(filename=/lustre03/project/6004655/COMMUN/soft/packages/comorment/mixer/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.run4.ld, numel=19295890)... 20230218 18:12:11.407822 >set_ld_r2_coo(chr_label=22, length=19295890); 20230218 18:12:11.459199 LdMatrixCsr::init_diagonal(chr_label=22) added 0 tag (out of 141123 snps) elements with r2=1.0 to the diagonal of LD r2 matrix 20230218 18:12:12.764309 <set_ld_r2_coo: done; (new_elements: 0), elapsed time 1307 ms 20230218 18:12:12.766229 >set_weights_randprune(n=64, r2=0.1, exclude=, extract=) 20230218 18:12:12.777641 <set_weights_randprune(n=64, r2=0.1, exclude=, extract=), elapsed time 11ms 20230218 18:12:12.778243 set_option(diag=0); 20230218 18:12:12.778351 diag: numsnp=9997231 20230218 18:12:12.778406 diag: numtag=0 20230218 18:12:12.778460 diag: LdMatrixCsr 23 chunks in total. Logging futher info for non-empty chunks only. 20230218 18:12:12.778524 diag: zvec1.size()=0 20230218 18:12:12.778578 diag: zvec1=[], nnz=0 20230218 18:12:12.778634 diag: nvec1.size()=0 20230218 18:12:12.778688 diag: nvec1=[], nnz=0 20230218 18:12:12.778743 diag: causalbetavec1.size()=0 20230218 18:12:12.778797 diag: causalbetavec1=[], nnz=0 20230218 18:12:12.778861 diag: zvec2.size()=0 20230218 18:12:12.778935 diag: zvec2=[], nnz=0 20230218 18:12:12.778991 diag: nvec2.size()=0 20230218 18:12:12.779044 diag: nvec2=[], nnz=0 20230218 18:12:12.779099 diag: causalbetavec2.size()=0 20230218 18:12:12.779153 diag: causalbetavec2=[], nnz=0 20230218 18:12:12.779208 diag: weights.size()=0 20230218 18:12:12.779261 diag: weights=[], nnz=0 20230218 18:12:12.779316 diag: mafvec.size()=9997231 20230218 18:12:12.779370 diag: mafvec=[0.911043, 0.911043, 0.945808, 0.811861, 0.811861, ...], nnz=9997231 20230218 18:12:12.792650 diag: options.kmax=20000 20230218 18:12:12.792710 diag: options.use_complete_tagindices=0 20230218 18:12:12.792769 diag: options.disable_snp_to_tagmap=0 20230218 18:12:12.792830 diag: options.maxcausals=100000 20230218 18:12:12.792884 diag: options.numcomponents=1 20230218 18:12:12.792937 diag: options.r2min=0 20230218 18:12:12.792995 diag: options.z1max=1e+10 20230218 18:12:12.793051 diag: options.z2max=1e+10 20230218 18:12:12.793107 diag: options.costcalculator=0 (Sampling) 20230218 18:12:12.793171 diag: options.auxoption=1 (Ezvec2) 20230218 18:12:12.793234 diag: options.cache_tagr2sum=no 20230218 18:12:12.793287 diag: options.seed_=123 20230218 18:12:12.793341 diag: options.cubature_abserror=0 20230218 18:12:12.793396 diag: options.cubature_relerror=1e-05 20230218 18:12:12.793452 diag: options.cubature_maxevals=1000 20230218 18:12:12.793506 diag: options.calc_kpdf=0 20230218 18:12:12.793559 diag: options.ld_formatversion=-1 20230218 18:12:12.793613 diag: options.retrieve_ld_sumtype=0 20230218 18:12:12.793666 diag: Estimated memory usage (total): 0 bytes 20230218 18:12:12.794132 retrieve_mafvec() 20230218 18:12:12.806116 retrieve_mafvec() 20230218 18:12:12.837644 runtime_error: arg <= 0
I tried this using the SCZ data that was included.