invalid value encountered in sqrt for methylation tensorQTL

[hsun3163]

Following error occurs when running methyl for chrom21. Shall take look at ``

Traceback (most recent call last):
  File "/mnt/vast/hpc/csg/molecular_phenotype_calling/tmpi874vmi3/singularity_run_38369.py", line 15, in <module>
    phenotype_df, phenotype_pos_df = tensorqtl.read_phenotype_bed(expression_bed)
  File "/opt/conda/lib/python3.8/site-packages/tensorqtl/core.py", line 381, in read_phenotype_bed
    raise ValueError("The BED file must define the TSS/cis-window center, with start+1 == end.")
ValueError: The BED file must define the TSS/cis-window center, with start+1 == end.
Mapping files: 100%|██████████| 3/3 [00:01<00:00,  1.54it/s]
/opt/conda/lib/python3.8/site-packages/tensorqtl/core.py:314: RuntimeWarning: invalid value encountered in sqrt
  return 2*stats.t.cdf(-np.abs(np.sqrt(tstat2)), dof)

However the result seems legit

hs3163@node42:/mnt/vast/hpc/csg/molecular_phenotype_calling$ head Methy.QTL_new/ROSMAP_arrayMethylation_covariates.sesame.methyl.beta.sample_matched.bed_BMIQ.bed.filter_na.bed.softImputed.bed.processed_phenotype.per_chrom_methy.peer.pca.chr21.norminal.cis_long_table.txt
molecular_trait_id      variant_id      tss_distance    ma_samples      ma_count        pvalue  beta    se      molecular_trait_object_id       maf     n       alt     ref     pos     chrom
cg23919830      chr21:9893625_G_A       -514378 74      74      0.44020792787262586     0.005262543     0.006813446     cg23919830      0.05648855119943619     655     A       G       9893625 chr21
cg23919830      chr21:9896000_CTTATA_C  -512003 517     624     0.7111190144230543      -0.0012996283   0.0035074262    cg23919830      0.47705698013305664     655     C       CTTATA  9896000 chr21
cg23919830      chr21:9902109_G_A       -505894 79      79      0.39228541206906287     0.005652037     0.006601902     cg23919830      0.06030534207820892     655     A       G       9902109 chr21
cg23919830      chr21:9908876_AC_A      -499127 128     128     0.924058158011328       -0.0005197538   0.005450162     cg23919830      0.09770992398262024     655     A       AC      9908876 chr21
cg23919830      chr21:9911734_G_A       -496269 245     264     0.21341978653064583     -0.004941255    0.003966993     cg23919830      0.20401853322982788     655     A       G       9911734 chr21
cg23919830      chr21:9912491_AC_A      -495512 53      53      0.7086564130205697      -0.0029034277   0.007766379     cg23919830      0.040458016097545624    655     A       AC      9912491 chr21
cg23919830      chr21:9916253_C_T       -491750 37      37      0.6216208579160541      0.0045962967    0.009307626     cg23919830      0.028244275599718094    655     T       C       9916253 chr21
cg23919830      chr21:9918044_T_C       -489959 127     127     0.7740394144606008      0.0015659303    0.005451836     cg23919830      0.09694656729698181     655     C       T       9918044 chr21
cg23919830      chr21:9918851_T_TA      -489152 121     121     0.11354790099213422     0.008763451     0.0055295085    cg23919830      0.09236641228199005     655     TA      T       9918851 chr21