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step1 KeyError: 'ID"

Open AEAEAESSC opened this issue 1 year ago • 0 comments

[INFO] @----------------------------------------------------------@ | HESS | v0.5 | 9/October/2017 | |----------------------------------------------------------|

(C) 2017 Huwenbo Shi, GNU General Public License, v3
For documentation, citation & bug-report instructions:
http://bogdan.bioinformatics.ucla.edu/software/hess/
   @----------------------------------------------------------@

[INFO] Command started at: Thu, 07 Dec 2023 09:05:39 [INFO] Command issued: hess.py
--bfile /home/zhanya/hess-hess-0.5/1kg_eur_1pct/1kg_eur_1pct_chr22
--local-rhog /external/zhanya/hess/mdd3.txt /external/zhanya/hess/whr4.txt
--partition /home/zhanya/hess-hess-0.5/fourier_ls-all.bed
--out /external/zhanya/hess/step1
--chrom 22 /home/zhanya/hess-hess-0.5/src/refpanel.py:13: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. partition = pd.read_table(filename, delim_whitespace=True) [INFO] Loaded 24 partitions on chromosome 22 [INFO] Average window size is 1466370 /home/zhanya/hess-hess-0.5/src/refpanel.py:61: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. names=['SNP', 'BP', 'A0', 'A1']) [INFO] 123295 SNPs read from reference panel [INFO] Loaded 132836 SNPs with rs IDs and single-letter alleles on chromosome 22 from the GWAS summary data file Traceback (most recent call last): File "hess.py", line 217, in main() File "hess.py", line 45, in main argmap['out']) File "/home/zhanya/hess-hess-0.5/src/estimation.py", line 390, in local_rhog_step1 sumstats1.filter_sumstats(refpanel.get_map()) File "/home/zhanya/hess-hess-0.5/src/sumstats.py", line 168, in filter_sumstats elif a1a0 in reverse[a1a2]: flip.append(i) KeyError: 'ID" This code only encountered a problem in the 22nd loop, reporting a KeyError: 'ID'. I used the same code to run 21 chromosomes before, and I don't know where the problem occurred here is my code: for chrom in $(seq 22) do python hess.py
--local-rhog /external/zhanya/hess/mdd3.txt /external/zhanya/hess/whr4.txt
--chrom $chrom
--bfile /home/zhanya/hess-hess-0.5/1kg_eur_1pct/1kg_eur_1pct_chr$chrom
--partition /home/zhanya/hess-hess-0.5/fourier_ls-all.bed
--out /external/zhanya/hess/step1 done

AEAEAESSC avatar Dec 07 '23 01:12 AEAEAESSC