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step1 KeyError: 'ID" #31

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AEAEAESSC opened this issue Dec 7, 2023 · 0 comments
Open

step1 KeyError: 'ID" #31

AEAEAESSC opened this issue Dec 7, 2023 · 0 comments

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@AEAEAESSC
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[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

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