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QTL Discovery using Annotations
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ERROR: Underflow #6

Closed sum732 closed 3 years ago

sum732 commented 3 years ago

Hello, I am trying to run torus for annotations and keeping getting following error message:

gsl: exp.c:113: ERROR: underflow
Default GSL error handler invoked.

Both the files are gzipped, here are the snippets for "qtl" files (space separated) 

ENSG00000227232.5 chr1_873251_G_A_b38 843698 0.000269876 -0.155466 0.042272
ENSG00000227232.5 chr1_873548_C_T_b38 843995 0.000268693 -0.155633 0.0423039
ENSG00000227232.5 chr1_878850_T_A_b38 849297 0.000827723 0.162463 0.0481966
ENSG00000237613.2 chr1_758351_A_G_b38 722270 0.00123578 0.257066 0.0789654
ENSG00000237613.2 chr1_758443_G_C_b38 722362 0.00123806 0.256932 0.0789371
ENSG00000237613.2 chr1_772142_G_C_b38 736061 0.000702205 0.270077 0.0790327
ENSG00000237613.2 chr1_792461_G_A_b38 756380 0.0012498 0.354901 0.109129
ENSG00000237613.2 chr1_794707_T_C_b38 758626 0.000744319 0.367051 0.107928
ENSG00000237613.2 chr1_830627_A_C_b38 794546 0.000820826 0.250443 0.0742443
ENSG00000237613.2 chr1_832873_A_C_b38 796792 0.00129901 -0.197681 0.0609971

and here is annotation file, for brevity showing first few cols

SNP     3_prime_UTR_variant_d   5_prime_UTR_variant_d   NMD_transcript_variant_d
chr1_722408_G_C_b38     0       0       0
chr1_727034_C_T_b38     0       0       1
chr1_727242_G_A_b38     0       1       0
chr1_727477_G_A_b38     0       1       0
chr1_727717_G_C_b38     0       0       0
chr1_736852_C_T_b38     1       0       0
chr1_758351_A_G_b38     1      0       1

Command used :

./torus -d TOP_50_SigPairs_eQTL.txt.gz --fastqtl -est -annot Unique_Consequences_Fixed.tsv.gz >TORUS_Enrichment_TOP_50 &> torus_100.log.txt

Any ideas how to fix this issue? Thanks

sum732 commented 3 years ago

Just thought of updating this issue. The issue was NOT memory availability. Turns out each feature ( eg. frameshift_variant, inframe_insertion etc), must have >100 1's. If there are less then that TORUS fails.