Step 1 Error

[bperry089]

Hi,

I'm receiving an error when looping through chromosomes and I wondered if you could help me figure it out?

[INFO] Loaded 133 partitions on chromosome 1
[INFO] Average window size is 1873901
[INFO] 39728178 SNPs read from reference panel
[INFO] Loaded 589535 SNPs with rs IDs and single-letter alleles on chromosome 1 from the GWAS summary data file
[INFO] 501348 SNPs left after filtering
[INFO] Loaded 183464 SNPs with rs IDs and single-letter alleles on chromosome 1 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 "/Users/benjaminperry/HESS/src/estimation.py", line 392, in local_rhog_step1
sumstats2.filter_sumstats(refpanel.get_map())
File "/Users/benjaminperry/HESS/src/sumstats.py", line 168, in filter_sumstats
elif a1a0 in reverse[a1a2]: flip.append(i)
KeyError: 'ag'

The same error is appearing on each chromosome as it loops through.

would really appreciate the advice!

Thanks

[huwenboshi]

Hi bperry089,

It seems some of the alleles in your summary stats file are in lower cases.

Please change those to upper cases, and see if the issue persists.

Sincerely,

Huwenbo Shi

[bperry089]

Hi

Thanks so much for the quick response. You are correct, one of the files had alleles in lower-case. I amended that and the script seems to progress, but there is a new error. I wonder if you could give your advice?

[INFO] 39728178 SNPs read from reference panel
[INFO] Loaded 638081 SNPs with rs IDs and single-letter alleles on chromosome 2 from the GWAS summary data file
[INFO] 537262 SNPs left after filtering
[INFO] Loaded 211326 SNPs with rs IDs and single-letter alleles on chromosome 2 from the GWAS summary data file
[INFO] 177488 SNPs left after filtering
[INFO] Loading fam file 1kg_phase1_all.fam
[INFO] Loading bim file 1kg_phase1_all.bim
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysnptools/pstreader/_subset.py:58: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
self._run_once()
[INFO] bed file is open 1kg_phase1_all.bed
Killed: 9

Thanks so much