partitioned LDSC error

[Patrick Sullivan]

Hi - ran into a cryptic error - not a python or numpy user so need a bit of help in trying to figure out what to do next. 

I have a new annotation to which I am trying to evaluate with the original Finucane 2015 model (not Gazal 2017). The first part of it went fine but crashed out here. full log appended below. Any ideas? thx in advance! best pfs

Reading annot matrix from /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_EUR_Phase3_baseline/baseline.,baseline.[1-22] ...

Traceback (most recent call last):

  File "/nas/longleaf/apps/ldsc/1.0.0/ldsc/ldsc.py", line 644, in <module>

    sumstats.estimate_h2(args, log)

  File "/nas/longleaf/apps/ldsc/1.0.0/ldsc/ldscore/sumstats.py", line 372, in estimate_h2

    df_results = hsqhat._overlap_output(ref_ld_cnames, overlap_matrix, M_annot, M_tot, args.print_coefficients)

  File "/nas/longleaf/apps/ldsc/1.0.0/ldsc/ldscore/regressions.py", line 398, in _overlap_output

    overlap_matrix_prop[i, :] = overlap_matrix[i, :] / M_annot

ValueError: operands could not be broadcast together with shapes (1,55) (1,54) 

*********************************************************************

* LD Score Regression (LDSC)

* Version 1.0.0

* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane

* Broad Institute of MIT and Harvard / MIT Department of Mathematics

* GNU General Public License v3

*********************************************************************

Call: 

./ldsc.py \

--h2 /nas/depts/007/sullilab/shared/gwasOmnibus/03sumstats/iq2018.sumstats.gz \

--ref-ld-chr /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_EUR_Phase3_baseline/baseline.,baseline. \

--out ../iq2018_BSG_McVicker2009.hg19.bed_Finucane_dir \

--overlap-annot  \

--frqfile-chr /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_Phase3_frq/1000G.EUR.QC. \

--w-ld-chr /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC. \

--print-coefficients  

Beginning analysis at Sat Mar 30 16:10:15 2019

Reading summary statistics from /nas/depts/007/sullilab/shared/gwasOmnibus/03sumstats/iq2018.sumstats.gz ...

Read summary statistics for 1196711 SNPs.

Reading reference panel LD Score from /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_EUR_Phase3_baseline/baseline

.,baseline.[1-22] ...

Read reference panel LD Scores for 1190321 SNPs.

Removing partitioned LD Scores with zero variance.

Reading regression weight LD Score from /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC.[1-22] ...

Read regression weight LD Scores for 1187349 SNPs.

After merging with reference panel LD, 1179404 SNPs remain.

After merging with regression SNP LD, 1176447 SNPs remain.

Removed 0 SNPs with chi^2 > 269.867 (1176447 SNPs remain)

Total Observed scale h2: 0.1635 (0.0058)

Categories: baseL2_0 Coding_UCSC.bedL2_0 Coding_UCSC.extend.500.bedL2_0 Conserved_LindbladToh.bedL2_0 Conserved_LindbladToh.extend.500.bedL2_0 CTCF_Hoffman.bedL2_0 CTCF_Hoffman.extend.500.bedL2_0 DGF_ENCODE.bedL2_0 DGF_ENCODE.extend.500.bedL2_0 DHS_peaks_Trynka.bedL2_0 DHS_Trynka.bedL2_0 DHS_Trynka.extend.500.bedL2_0 Enhancer_Andersson.bedL2_0 Enhancer_Andersson.extend.500.bedL2_0 Enhancer_Hoffman.bedL2_0 Enhancer_Hoffman.extend.500.bedL2_0 FetalDHS_Trynka.bedL2_0 FetalDHS_Trynka.extend.500.bedL2_0 H3K27ac_Hnisz.bedL2_0 H3K27ac_Hnisz.extend.500.bedL2_0 H3K27ac_PGC2.bedL2_0 H3K27ac_PGC2.extend.500.bedL2_0 H3K4me1_peaks_Trynka.bedL2_0 H3K4me1_Trynka.bedL2_0 H3K4me1_Trynka.extend.500.bedL2_0 H3K4me3_peaks_Trynka.bedL2_0 H3K4me3_Trynka.bedL2_0 H3K4me3_Trynka.extend.500.bedL2_0 H3K9ac_peaks_Trynka.bedL2_0 H3K9ac_Trynka.bedL2_0 H3K9ac_Trynka.extend.500.bedL2_0 Intron_UCSC.bedL2_0 Intron_UCSC.extend.500.bedL2_0 PromoterFlanking_Hoffman.bedL2_0 PromoterFlanking_Hoffman.extend.500.bedL2_0 Promoter_UCSC.bedL2_0 Promoter_UCSC.extend.500.bedL2_0 Repressed_Hoffman.bedL2_0 Repressed_Hoffman.extend.500.bedL2_0 SuperEnhancer_Hnisz.bedL2_0 SuperEnhancer_Hnisz.extend.500.bedL2_0 TFBS_ENCODE.bedL2_0 TFBS_ENCODE.extend.500.bedL2_0 Transcribed_Hoffman.bedL2_0 Transcribed_Hoffman.extend.500.bedL2_0 TSS_Hoffman.bedL2_0 TSS_Hoffman.extend.500.bedL2_0 UTR_3_UCSC.bedL2_0 UTR_3_UCSC.extend.500.bedL2_0 UTR_5_UCSC.bedL2_0 UTR_5_UCSC.extend.500.bedL2_0 WeakEnhancer_Hoffman.bedL2_0 WeakEnhancer_Hoffman.extend.500.bedL2_0 BSG_McVicker2009.hg19.bed_500bp_extL2_1

Lambda GC: 1.7218

Mean Chi^2: 2.0359

Intercept: 1.0649 (0.0116)

Ratio: 0.0627 (0.0112)

Reading annot matrix from /nas/depts/007/sullilab/shared/partitioned_LDSC/1000G_EUR_Phase3_baseline/baseline.,baseline.[1-22] ...

Traceback (most recent call last):

  File "/nas/longleaf/apps/ldsc/1.0.0/ldsc/ldsc.py", line 644, in <module>

    sumstats.estimate_h2(args, log)

  File "/nas/longleaf/apps/ldsc/1.0.0/ldsc/ldscore/sumstats.py", line 372, in estimate_h2

    df_results = hsqhat._overlap_output(ref_ld_cnames, overlap_matrix, M_annot, M_tot, args.print_coefficients)

  File "/nas/longleaf/apps/ldsc/1.0.0/ldsc/ldscore/regressions.py", line 398, in _overlap_output

    overlap_matrix_prop[i, :] = overlap_matrix[i, :] / M_annot

ValueError: operands could not be broadcast together with shapes (1,55) (1,54) 

Analysis finished at Sat Mar 30 16:13:15 2019

Total time elapsed: 3.0m:0.04s

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