Assertion Error when using functional susie fine mappping

[dietina]

Hi Omer,

Can I know if we have some advice on how to fix this AssertionError ? :

Traceback (most recent call last): File "/filepath/finemapper.py", line 1262, in residual_var=args.susie_resvar, residual_var_init=args.susie_resvar_init, hess_resvar=args.susie_resvar_hess) File "/filepath/finemapper.py", line 743, in finemap assert np.isclose(prior_weights.sum(), 1) AssertionError

I used functional susie finemapping, and this issue happens in some certain CHRs, for example, CHR6 and CHR1, but it worked for CHR2 and CHR5. I have not encountered the issue when I ran non-functional susie finemapping for all CHRs(1-22).

Any advice would be appreciated! Thank you in advance Omer.

[omerwe]

Hi @dietina, I would need more information to help reproduce this... Can you run the example pipeline without an error? If yes, can you please prepare a short reproducible example that I can look at?

[dietina]

Thank you Omer! Yes I can run the pipeline code, and I am only having this issue on CHR 1, 6 and 11 in my real dataset. Other CHRs worked perfectly fine. I tried individual command (paste from .jobs txt) using Python command, however it gave me the same Assertation Error.

Can I know if I can send the data to your email?

Thank you!

[omerwe]

@dietina, you can send example data to [email protected]. I suspect that this is somehow related to long-range LD regions: Both chromosomes 6 and 11 have such regions (as well as chromosome 8). However, I'm not aware of any long-range LD regions for chromosome 1...

[liqingbioinfo]

May I know the follow-ups for this issue? I encountered the same problem for chromosome 6. Is there any way to fix it?

[omerwe]

@liqingbioinfo please feel free to send me a reproducible example, and I'll try looking into it

[dietina]

Hi Omer and Liqing, sorry I was not able to login during the past days. This issue has not been fixed. I will come up with the example and send this to Omer. I am sorry for the delay. Can I know if there is any updates that may help with the issue? Thank you! @omerwe @liqingbioinfo

[omerwe]

Sorry, I can't do anything until I have a reproducible example in hand...

[keyrunad]

I have the same error for the job below:

python3 finemapper.py --chr 1 --geno ../1000G_EUR_Phase3_plink/1000G.EUR.QC.1 --start 140000001 --end 143000001 --out ../outputs/polyfun_all.chr1.140000001_143000001.gz --method susie --sumstats ../polyfun_sumstats --n 321498 --memory 1 --max-num-causal 5 --allow-missing

The reason seems to be df_sumstats_locus not having any rows except the header causing prior_weights at line 749 of finemapper.py to be empty and its sum to be 0. Happy to provide any other details if needed. Thanks in advance for all your help!

[omerwe]

@keyrunad thanks for looking into this. I updated the code to verify that df_sumstats_locus is not empty, which should at least print a more relevant error message (can you please git pull and make sure that it does)?

However, I still don't know where the error is coming from. I suspect that it's because the SNPs in the LD file and in the sumstats file are inconsistent, but I can't say more until I see a reproducible example, or at least a snapshot of the relevant files. If you can send these to me (see my email address at previous messages in this thread) that would be great.

[noeri-mohamed-hoesein]

Hi Omer, I also seem to be encountering a similar error with functional susie fine mapping:

Mapping files:   0%|          | 0/3 [00:00<?, ?it/s]
Mapping files:  33%|███▎      | 1/3 [00:04<00:09,  4.84s/it]
Mapping files:  67%|██████▋   | 2/3 [00:05<00:02,  2.25s/it]
Mapping files: 100%|██████████| 3/3 [00:06<00:00,  1.82s/it]
Mapping files: 100%|██████████| 3/3 [00:06<00:00,  2.19s/it]

  0%|          | 0/1 [00:00<?, ?it/s]
100%|██████████| 1/1 [00:04<00:00,  4.97s/it]
100%|██████████| 1/1 [00:04<00:00,  4.97s/it]
Traceback (most recent call last):
  File "/.../software/polyfun/finemapper.py", line 1275, in <module>
    df_finemap = finemap_obj.finemap(locus_start=args.start, locus_end=args.end, num_causal_snps=args.max_num_causal,
  File "/.../software/polyfun/finemapper.py", line 755, in finemap
    assert np.isclose(prior_weights.sum(), 1)
AssertionError

This is the command I'm using:

python /.../polyfun/finemapper.py \
    --geno /LD_reference_AFR_chr5 \
    --sumstats /.../polyfun.snpvar.men.afr.out \
    --n 1709 \
    --chr 5 \
    --start 75935061 \
    --end 76217073 \
    --method susie \
    --max-num-causal 10 \
    --cache-dir /.../LD_cache \
    --out /.../SuSiE_output/finemap.men.afr.5.7593506.76217073.L10.gz \
    --allow-missing \
    --allow-swapped-indel-alleles

But it only keeps happening in certain regions of chr 6 and chr 5. Do you have any advice on how I can fix this?

[omerwe]

As I wrote in the past, I can't fix this unless someone can send me a reproducible example, sorry...

[noeri-mohamed-hoesein]

If this email [email protected] is still in use I can send you the data with which I got this error

[omerwe]

sure