segfault

[yhuang11-ilmn]

Hello,

Similar to an earlier issue #242 I got into this segfault error when it was trying to reading the summary stats:

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<>
<> MTAG: Multi-trait Analysis of GWAS
<> Version: 1.0.8
<> (C) 2017 Omeed Maghzian, Raymond Walters, and Patrick Turley
<> Harvard University Department of Economics / Broad Institute of MIT and Harvard
<> GNU General Public License v3
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<> Note: It is recommended to run your own QC on the input before using this program.
<> Software-related correspondence: jjala.ssgac@gmail.com
<> All other correspondence: paturley@broadinstitute.org
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Calling ./mtag.py
--z-name Z
--stream-stdout
--n-name N
--a2-name A2
--a1-name A1
--snp-name SNP
--sumstats /my/path/EUR_Phe_411_4_with_z.tsv,/my/path/EUR_Phe_250_2_with_z.tsv
--chunksize 10000
--out ./CAD_MTAG

Beginning MTAG analysis...
MTAG will use the Z column for analyses.
Read in Trait 1 summary statistics (26175912 SNPs) from /my/path/EUR_Phe_411_4_with_z.tsv ...
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Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><
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Interpreting column names as follows:
N: Sample size
A1: a1, interpreted as ref allele for signed sumstat.
p: p-Value
A2: a2, interpreted as non-ref allele for signed sumstat.
SNP: Variant ID (e.g., rs number)
Z: Directional summary statistic as specified by --signed-sumstats.
se: Standard errors of BETA coefficients

Reading sumstats from provided DataFrame into memory 10000 SNPs at a time.
WARNING: 1 SNPs had P outside of (0,1]. The P column may be mislabeled.
Read 26175912 SNPs from --sumstats file.
Removed 0 SNPs with missing values.
Removed 0 SNPs with INFO <= None.
Removed 0 SNPs with MAF <= 0.01.
Removed 0 SNPs with SE <0 or NaN values.
Removed 1 SNPs with out-of-bounds p-values.
Removed 2334257 variants that were not SNPs. Note: strand ambiguous SNPs were not dropped.
23841654 SNPs remain.
/cm/local/apps/sge/var/spool/sd-rnd005/job_scripts/2936827: line 33: 219432 Segmentation fault (core dumped) python /my/path/mtag/mtag.py --sumstats "$Phe_411_4_with_z","$Phe_250_2_with_z" --out ./CAD_MTAG --snp_name SNP --a1_name A1 --a2_name A2 --eaf_name freq --z_name Z --n_name N --chunksize 10000 --stream_stdout

As the segfault doesn't show detailed trace, it is a bit difficult for me to figure out what went wrong. I am guessing there might be some incompatibility between my pandas and numpy installation. Could you share the version number of these packages that you have been using and were proven to work? Thank you.

[JonJala]

In the environment.yml file, it lists:

• numpy>=1.13.1
• pandas>=0.18.1

So you could try those versions if you have them available.

You may want to check your sumstats files that are being processed, as well (looks like it's still likely on the first one, so I'd start there, but you'll probably want to check the other as well) to make sure there's nothing too crazy with it that is causing Pandas or Numpy to crash (they shouldn't do that and should handle errors gracefully, of course, but in the scheme of things, it's probably faster to doublecheck the data, even if you submit a bug report later)