fgvieira/ngsLD

ngsLD sometimes hangs indefinitely

James-S-Santangelo opened this issue · 8 comments

James-S-Santangelo commented

Hello!

I've come across an interesting issue where ngsLD will sometimes hang on "Reading data from file..." and never proceed any further, even after approximately 48 hours.

I noticed this problem while estimate pairwise LD in parallel across 16 separate chromosomes. Some chromosomes would finish within a couple hours, while others would just hang and eventually get terminated by the cluster due to timing out.

I'm estimating pairwise LD from genotype likelihoods that I calculated in ANGSD using the following command:

 angsd -GL 1 \      
        -out {0}/angsd/{{wildcards.chrom}}/{{wildcards.chrom}}_genolike_allSamples \
        -nThreads {{threads}} \
        -doGlf 2 \     
        -doMajorMinor 1 \
        -SNP_pval 1e-6 \
        -doMaf 1 \     
        -doCounts 1 \  
        -setMinDepthInd 3 \
        -setMaxDepth 4500 \
        -baq 2 \
        -ref {1} \
        -minInd 96 \
        -minQ 20 \
        -minMapQ 30 \
        -doSaf 1 \
        -anc {1} \
        -r {{wildcards.chrom}} \
        -bam {{input.bams}} 2> {{log}}

This command succeeds without issue for all chromosomes and generates all output files, including the BEAGLE format genotype likelihoods used as input to ngsLD. Here are the first 10 lines of one of these files:

marker	allele1	allele2	Ind0	Ind0	Ind0	Ind1	Ind1	Ind1	Ind2	Ind2	Ind2	Ind3	Ind3	Ind3	Ind4	Ind4	Ind4	Ind5	Ind5	Ind5	Ind6	Ind6	Ind6	Ind7	Ind7	Ind7	Ind8	Ind8	Ind8	Ind9	Ind9	Ind9	Ind10	Ind10	Ind10	Ind11	Ind11	Ind11	Ind12	Ind12	Ind12	Ind13	Ind13	Ind13	Ind14	Ind14	Ind14	Ind15	Ind15	Ind15	Ind16	Ind16	Ind16	Ind17	Ind17	Ind17	Ind18	Ind18	Ind18	Ind19	Ind19	Ind19	Ind20	Ind20	Ind20	Ind21	Ind21	Ind21	Ind22	Ind22	Ind22	Ind23	Ind23	Ind23	Ind24	Ind24	Ind24	Ind25	Ind25	Ind25	Ind26	Ind26	Ind26	Ind27	Ind27	Ind27	Ind28	Ind28	Ind28	Ind29	Ind29	Ind29	Ind30	Ind30	Ind30	Ind31	Ind31	Ind31	Ind32	Ind32	Ind32	Ind33	Ind33	Ind33	Ind34	Ind34	Ind34	Ind35	Ind35	Ind35	Ind36	Ind36	Ind36	Ind37	Ind37	Ind37	Ind38	Ind38	Ind38	Ind39	Ind39	Ind39	Ind40	Ind40	Ind40	Ind41	Ind41	Ind41	Ind42	Ind42	Ind42	Ind43	Ind43	Ind43	Ind44	Ind44	Ind44	Ind45	Ind45	Ind45	Ind46	Ind46	Ind46	Ind47	Ind47	Ind47	Ind48	Ind48	Ind48	Ind49	Ind49	Ind49	Ind50	Ind50	Ind50	Ind51	Ind51	Ind51	Ind52	Ind52	Ind52	Ind53	Ind53	Ind53	Ind54	Ind54	Ind54	Ind55	Ind55	Ind55	Ind56	Ind56	Ind56	Ind57	Ind57	Ind57	Ind58	Ind58	Ind58	Ind59	Ind59	Ind59	Ind60	Ind60	Ind60	Ind61	Ind61	Ind61	Ind62	Ind62	Ind62	Ind63	Ind63	Ind63	Ind64	Ind64	Ind64	Ind65	Ind65	Ind65	Ind66	Ind66	Ind66	Ind67	Ind67	Ind67	Ind68	Ind68	Ind68	Ind69	Ind69	Ind69	Ind70	Ind70	Ind70	Ind71	Ind71	Ind71	Ind72	Ind72	Ind72	Ind73	Ind73	Ind73	Ind74	Ind74	Ind74	Ind75	Ind75	Ind75	Ind76	Ind76	Ind76	Ind77	Ind77	Ind77	Ind78	Ind78	Ind78	Ind79	Ind79	Ind79	Ind80	Ind80	Ind80	Ind81	Ind81	Ind81	Ind82	Ind82	Ind82	Ind83	Ind83	Ind83	Ind84	Ind84	Ind84	Ind85	Ind85	Ind85	Ind86	Ind86	Ind86	Ind87	Ind87	Ind87	Ind88	Ind88	Ind88	Ind89	Ind89	Ind89	Ind90	Ind90	Ind90	Ind91	Ind91	Ind91	Ind92	Ind92	Ind92	Ind93	Ind93	Ind93	Ind94	Ind94	Ind94	Ind95	Ind95	Ind95	Ind96	Ind96	Ind96	Ind97	Ind97	Ind97	Ind98	Ind98	Ind98	Ind99	Ind99	Ind99	Ind100	Ind100	Ind100	Ind101	Ind101	Ind101	Ind102	Ind102	Ind102	Ind103	Ind103	Ind103	Ind104	Ind104	Ind104	Ind105	Ind105	Ind105	Ind106	Ind106	Ind106	Ind107	Ind107	Ind107	Ind108	Ind108	Ind108	Ind109	Ind109	Ind109	Ind110	Ind110	Ind110	Ind111	Ind111	Ind111	Ind112	Ind112	Ind112	Ind113	Ind113	Ind113	Ind114	Ind114	Ind114	Ind115	Ind115	Ind115	Ind116	Ind116	Ind116	Ind117	Ind117	Ind117	Ind118	Ind118	Ind118	Ind119	Ind119	Ind119
CM019102.1_30951	2	0	0.984616	0.015384	0.000000	0.998051	0.001949	0.000000	0.999992	0.000008	0.000000	0.999512	0.000488	0.000000	0.996109	0.003891	0.000000	0.333333	0.333333	0.333333	0.333333	0.333333	0.333333	0.969698	0.030302	0.000000	0.000041	0.999959	0.000000	0.999024	0.000976	0.000000	0.999024	0.000976	0.000000	0.996109	0.003891	0.000000	0.998051	0.001949	0.000000	0.333333	0.333333	0.333333	0.399098	0.600902	0.000000	0.999878	0.000122	0.000000	0.941178	0.058822	0.000000	0.010308	0.989692	0.000000	0.999512	0.000488	0.000000	0.992249	0.007751	0.000000	0.996109	0.003891	0.000000	0.092094	0.907906	0.000000	0.001593	0.998406	0.000000	0.333333	0.333333	0.333333	0.333333	0.333333	0.333333	0.333333	0.333333	0.333333	0.142436	0.857564	0.000000	0.999756	0.000244	0.000000	0.999969	0.000031	0.000000	0.024890	0.975110	0.000000	0.999024	0.000976	0.000000	0.992249	0.007751	0.000000	0.333333	0.333333	0.333333	0.449468	0.550532	0.000000	0.000020	0.999980	0.000000	0.076885	0.923115	0.000000	0.888891	0.111109	0.000000	0.006310	0.993690	0.000000	0.996109	0.003891	0.000000	0.998051	0.001949	0.000000	0.024890	0.975110	0.000000	0.999756	0.000244	0.000000	0.333333	0.333333	0.333333	0.333333	0.333333	0.333333	0.000001	0.999999	0.000000	0.765539	0.234461	0.000000	0.999939	0.000061	0.000000	0.000020	0.999980	0.000000	0.000073	0.999927	0.000000	0.998051	0.001949	0.000000	0.941178	0.058822	0.000000	0.941178	0.058822	0.000000	0.888891	0.111109	0.000000	0.999985	0.000015	0.000000	0.888891	0.111109	0.000000	0.999024	0.000976	0.000000	0.969698	0.030302	0.000000	0.984616	0.015384	0.000000	0.333333	0.333333	0.333333	0.024890	0.975110	0.000000	0.333333	0.333333	0.333333	0.169534	0.830466	0.000000	0.984616	0.015384	0.000000	0.941178	0.058822	0.000000	0.169534	0.830466	0.000000	0.969698	0.030302	0.000000	0.999512	0.000488	0.000000	0.999024	0.000976	0.000000	0.888891	0.111109	0.000000	0.992249	0.007751	0.000000	0.333333	0.333333	0.333333	0.984616	0.015384	0.000000	0.333333	0.333333	0.333333	0.992249	0.007751	0.000000	0.941178	0.058822	0.000000	0.999756	0.000244	0.000000	0.048566	0.951434	0.000000	0.941178	0.058822	0.000000	0.984616	0.015384	0.000000	0.333333	0.333333	0.333333	0.761488	0.238512	0.000000	0.984616	0.015384	0.000000	0.333333	0.333333	0.333333	0.999024	0.000976	0.000000	0.984616	0.015384	0.000000	0.333333	0.333333	0.333333	0.888891	0.111109	0.000000	0.333333	0.333333	0.333333	0.289899	0.710101	0.000000	0.888891	0.111109	0.000000	0.004109	0.995891	0.000000	0.000013	0.999987	0.000000	0.984616	0.015384	0.000000	0.992249	0.007751	0.000000	0.996109	0.003891	0.000000	0.969698	0.030302	0.000000	0.888891	0.111109	0.000000	0.449468	0.550532	0.000000	0.000081	0.999919	0.000000	0.000003	0.999997	0.000000	0.992249	0.007751	0.000000	0.000000	1.000000	0.000000	0.941178	0.058822	0.000000	0.999939	0.000061	0.000000	0.999878	0.000122	0.000000	0.941178	0.058822	0.000000	0.992249	0.007751	0.000000	0.048566	0.951434	0.000000	0.999996	0.000004	0.000000	0.074818	0.925182	0.000000	0.999512	0.000488	0.000000	0.000000	1.000000	0.000000	0.992249	0.007751	0.000000	0.998051	0.001949	0.000000	0.996109	0.003891	0.000000	0.999024	0.000976	0.000000	0.992249	0.007751	0.000000	0.996109	0.003891	0.000000	0.984616	0.015384	0.000000	0.000010	0.999990	0.000000
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CM019102.1_30984	1	2	1.000000	0.000000	0.000000	0.000000	1.000000	0.000000	1.000000	0.000000	0.000000	0.999713	0.000287	0.000000	0.999985	0.000015	0.000000	0.984616	0.015384	0.000000	0.996109	0.003891	0.000000	1.000000	0.000000	0.000000	0.000000	1.000000	0.000000	0.002598	0.997402	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999992	0.000008	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.941178	0.058822	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.990515	0.009485	0.000000	0.999024	0.000976	0.000000	0.996463	0.003537	0.000000	0.101860	0.898140	0.000000	0.000322	0.999678	0.000000	0.969698	0.030302	0.000000	0.999939	0.000061	0.000000	0.994593	0.005407	0.000000	1.000000	0.000000	0.000000	0.999428	0.000572	0.000000	0.399779	0.600221	0.000000	0.999998	0.000002	0.000000	0.999969	0.000031	0.000000	0.941178	0.058822	0.000000	0.000000	1.000000	0.000000	0.000253	0.999747	0.000000	0.000000	1.000000	0.000000	0.000128	0.999872	0.000000	0.969698	0.030302	0.000000	0.999985	0.000015	0.000000	0.999998	0.000002	0.000000	0.001523	0.998477	0.000000	1.000000	0.000000	0.000000	0.333333	0.333333	0.333333	0.984616	0.015384	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.881719	0.118281	0.000000	0.955158	0.044842	0.000000	0.942591	0.057409	0.000000	0.000025	0.999975	0.000000	0.249851	0.750149	0.000000	0.999969	0.000031	0.000000	1.000000	0.000000	0.000000	0.992249	0.007751	0.000000	0.000000	1.000000	0.000000	0.727041	0.272959	0.000000	0.493040	0.506960	0.000000	0.984616	0.015384	0.000000	0.000013	0.999987	0.000000	0.333333	0.333333	0.333333	0.977062	0.022938	0.000000	0.064072	0.935928	0.000000	0.002598	0.997402	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999024	0.000976	0.000000	1.000000	0.000000	0.000000	0.333333	0.333333	0.333333	0.000008	0.999992	0.000000	0.333333	0.333333	0.333333	1.000000	0.000000	0.000000	0.998051	0.001949	0.000000	1.000000	0.000000	0.000000	0.000326	0.999674	0.000000	0.188440	0.811560	0.000000	0.999985	0.000015	0.000000	0.000161	0.999839	0.000000	0.999996	0.000004	0.000000	0.249851	0.750149	0.000000	0.969698	0.030302	0.000000	0.727041	0.272959	0.000000	0.999024	0.000976	0.000000	0.990231	0.009769	0.000000	0.999939	0.000061	0.000000	0.333333	0.333333	0.333333	0.777190	0.222810	0.000000	0.371164	0.628836	0.000000	0.998083	0.001917	0.000000	0.001301	0.998699	0.000000	0.999939	0.000061	0.000000	0.000773	0.999227	0.000000	1.000000	0.000000	0.000000	0.999512	0.000488	0.000000	0.000041	0.999959	0.000000	0.000400	0.999600	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999756	0.000244	0.000000	0.999985	0.000015	0.000000	0.999998	0.000002	0.000000	0.000000	1.000000	0.000000	0.118420	0.881580	0.000000	0.000009	0.999991	0.000000	0.914174	0.085826	0.000000	0.999969	0.000031	0.000000	0.867191	0.132809	0.000000	0.000000	1.000000	0.000000	1.000000	0.000000	0.000000	0.399779	0.600221	0.000000	0.963560	0.036440	0.000000	0.999512	0.000488	0.000000	0.991127	0.008873	0.000000
CM019102.1_30985	3	1	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.928866	0.071134	0.000000	0.984616	0.015384	0.000000	0.048566	0.951434	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.867191	0.132809	0.000000	1.000000	0.000000	0.000000	0.000000	1.000000	0.000000	1.000000	0.000000	0.000000	0.999992	0.000008	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.024890	0.975110	0.000000	1.000000	0.000000	0.000000	0.999995	0.000005	0.000000	0.999395	0.000605	0.000000	0.999024	0.000976	0.000000	1.000000	0.000000	0.000000	0.999512	0.000488	0.000000	0.999024	0.000976	0.000000	0.984616	0.015384	0.000000	0.999939	0.000061	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999701	0.000299	0.000000	0.999999	0.000001	0.000000	0.928866	0.071134	0.000000	0.047944	0.952056	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.984616	0.015384	0.000000	0.999996	0.000004	0.000000	0.995235	0.004765	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.333333	0.333333	0.333333	0.984616	0.015384	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.998804	0.001196	0.000000	1.000000	0.000000	0.000000	0.999939	0.000061	0.000000	1.000000	0.000000	0.000000	0.996109	0.003891	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.992249	0.007751	0.000000	0.399779	0.600221	0.000000	0.333333	0.333333	0.333333	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999996	0.000004	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999963	0.000037	0.000000	0.999024	0.000976	0.000000	0.997611	0.002389	0.000000	0.333333	0.333333	0.333333	0.999999	0.000001	0.000000	0.333333	0.333333	0.333333	1.000000	0.000000	0.000000	0.999024	0.000976	0.000000	1.000000	0.000000	0.000000	0.999969	0.000031	0.000000	1.000000	0.000000	0.000000	0.999939	0.000061	0.000000	0.996109	0.003891	0.000000	0.000178	0.999822	0.000000	1.000000	0.000000	0.000000	0.969698	0.030302	0.000000	0.999963	0.000037	0.000000	0.998051	0.001949	0.000000	0.999969	0.000031	0.000000	0.999969	0.000031	0.000000	0.333333	0.333333	0.333333	1.000000	0.000000	0.000000	0.999998	0.000002	0.000000	1.000000	0.000000	0.000000	0.999992	0.000008	0.000000	0.999969	0.000031	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999756	0.000244	0.000000	0.999756	0.000244	0.000000	1.000000	0.000000	0.000000	0.999981	0.000019	0.000000	1.000000	0.000000	0.000000	0.076885	0.923115	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.000163	0.999837	0.000000	0.010308	0.989692	0.000000	0.999999	0.000001	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.942420	0.057580	0.000000	0.999996	0.000004	0.000000	1.000000	0.000000	0.000000	1.000000	0.000000	0.000000	0.999701	0.000299	0.000000	1.000000	0.000000	0.000000	0.000501	0.999499	0.000000	1.000000	0.000000	0.000000

Here is the ngsLD command that I've been running:

( NUM_SITES=$(cat {input.pos} | wc -l) &&                                                                                                                                                                                                                         
  ngsLD --geno {input.gls} \
        --pos {input.pos} \
        --n_ind 120 \
        --n_sites $NUM_SITES \
        --probs \
        --n_threads {threads} \
        --max_kb_dist 25 | gzip --best > {output} ) 2> {log}

where the first few lines of the position file looks like:

CM019102.1	30951
CM019102.1	30958
CM019102.1	30963
CM019102.1	30964
CM019102.1	30969
CM019102.1	30981
CM019102.1	30983
CM019102.1	30984
CM019102.1	30985
CM019102.1	30989

For reference, here is what the log file looks like for a successful run:

==> Input Arguments:
	geno: ../results/population_structure/angsd_gl/full/CM019101.1/CM019101.1_genolike_allSamples.beagle.gz
	probs: true
	log_scale: false
	n_ind: 120
	n_sites: 2487093
	pos: ../results/population_structure/angsd_gl/full/CM019101.1/CM019101.1_angsdGL.pos (WITHOUT header)
	max_kb_dist (kb): 25
	max_snp_dist: 0
	min_maf: 0.001000
	ignore_miss_data: false
	call_geno: false
	N_thresh: 0.000000
	call_thresh: 0.000000
	rnd_sample: 1.000000
	seed: 1609882280
	extend_out: false
	out: (null) (WITHOUT header)
	n_threads: 16
	verbose: 1
	version: 1.1.1 (Dec 22 2020 @ 00:24:22)

==> GZIP input file (not BINARY)
> Reading data from file...
> Header found! Skipping line...
==> Calculating MAF for all sites...
==> Getting sites coordinates
==> Launching threads...
==> Waiting for all threads to finish...
==> Freeing memory...
Done!

And here is what the log file looks like for a failed run that hangs indefinitely:

==> Input Arguments:
	geno: ../results/population_structure/angsd/CM019105.1/CM019105.1_genolike_allSamples.beagle.gz
	probs: true
	log_scale: false
	n_ind: 120
	n_sites: 2036161
	pos: ../results/population_structure/angsd/CM019105.1/CM019105.1_angsdGL.pos (WITHOUT header)
	max_kb_dist (kb): 25
	max_snp_dist: 0
	min_maf: 0.001000
	ignore_miss_data: false
	call_geno: false
	N_thresh: 0.000000
	call_thresh: 0.000000
	rnd_sample: 1.000000
	seed: 1610049659
	extend_out: false
	out: (null) (WITHOUT header)
	n_threads: 16
	verbose: 1
	version: 1.1.1 (Dec 22 2020 @ 00:24:22)

==> GZIP input file (not BINARY)
> Reading data from file...

Finally, I should mention that the commands are being run inside of a singularity container (see HERE) into which I've installed ngsLD.

Also, it doesn't appear to be a problem with particular chromosomes. If I restart the failed runs, they will eventually succeed so I'm not sure what is causing the occasional hanging.

Thanks!

fgvieira commented

Hi James,

and sorry for the late reply.

This is indeed strange, specially since you say that these failed runs eventually finish, if you launch them again, right?

That makes me think that it might not be ngsLD related.
Can you check if you have enough memory to launch the 16 chromosome separately? If you don't, you might be using SWAP memory that is considerably slower.

TeresaPegan commented

This is happening to me as well, in a slightly different way. I have over 100 datasets with the same number of SNPs in each (from different species and different chromosomes -- I use the same size of subsample of SNPs from each), and all of them run nicely except for one, which hangs indefinitely. In my case, it is one particular dataset that hangs every time.
I know this might be difficult to troubleshoot, I could potentially send some data if it would help.
Thanks,
-Teresa

TeresaPegan commented

It's possible that my issue is caused by an input beagle file that is composed of mostly missing data (the vast majority of genotype likelihoods were 0.33333). Could it be getting stuck because of that?

fgvieira commented

Is it stuck (as in, no output being generated), or is it just slow?

TeresaPegan commented

It seems to get stuck -- I haven't let it run for more than 20 hours before killing it, but this is on a dataset of a size that typically takes about 10 minutes to run, so I don't think it's doing anything.

TeresaPegan commented

I was able to get it to complete when I add the options --min_maf 0 and --ignore_miss_data. Obviously this particular dataset is pretty worthless, it's mostly missing, but hopefully it's helpful to reveal a particular circumstance that can cause ngsLD to hang up and never finish!