Issue with bgen vs bed - Githubissues

choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

http://prsice.info

GNU General Public License v3.0

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Issue with bgen vs bed #257

Closed batzler closed 3 years ago

batzler commented 3 years ago

Version PRSice 2.2.10.b (2019-10-09)

When I submit a PRS job using the above version with bgen data I get the error below. PRSice executes as far as the clumping process then fails. However if I convert my bgen file to binary, I do NOT get the error. Any idea what issue PRSice is having with my bgen file? My bgen file was created from TopMed imputation server VCF output, using dosage=DS and --export bgen-1.2 Thanks in advance

Error Log Start performing clumping

773957 MB RAM detected; reserving 1 MB for clumping

Allocated 1 MB successfully

Clumping Progress: 0.00% glibc detected /research/bsi/tools/biotools/prsice/2.2.10.b/bin/PRSice_linux: free(): invalid next size (fast): 0x00002b0fba9d3210 *** ======= Backtrace: ========= [0x5da392] [0x46e2cc] [0x422413] [0x4044e3] [0x5ba7c6] [0x404a15] ======= Memory map: ======== 00400000-006cb000 r-xp 00000000 00:2b 103342084647 /research/bsi/tools/biotools/prsice/2.2.10.b/bin/PRSice_linux 008cb000-008d5000 rw-p 002cb000 00:2b 103342084647 /research/bsi/tools/biotools/prsice/2.2.10.b/bin/PRSice_linux 008d5000-00960000 rw-p 00000000 00:00 0 01b4d000-21b25000 rw-p 00000000 00:00 0 [heap] 2b0faea23000-2b0fb3423000 rw-p 00000000 00:00 0 2b0fb349b000-2b0fb5189000 rw-p 00000000 00:00 0 2b0fb7e17000-2b0fd2f93000 rw-p 00000000 00:00 0 7ffda22f6000-7ffda231b000 rw-p 00000000 00:00 0 [stack] 7ffda2325000-7ffda2327000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Error: Execution halted

batzler commented 3 years ago

Additionally, I've successfully used the UKB bgen files to run PRSice. So its the creation of bgen files from the Michigan imputation server VCF's that is presenting a problem. Thanks, Tony

choishingwan commented 3 years ago

Likely memory problem. 2.2.10 is rather old so I can't remember what exactly are the problem. If you use the latest version (2.3.3), then it should work with bgen file as long as you use --allow-inter option. (currently there's a bug that prevent bgen analysis without --allow-inter)

Sam

On Wed, Feb 17, 2021 at 5:29 PM batzler notifications@github.com wrote:

Additionally, I've successfully used the UKB bgen files to run PRSice. So its the creation of bgen files from the Michigan imputation server VCF's that is presenting a problem. Thanks, Tony

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/257#issuecomment-780896789, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYTM6RQIWA355Z5DGSLS7Q7LPANCNFSM4XZFSKTA .

batzler commented 3 years ago

Ok, Thank you. Will work on getting the most recent version downloaded and give that a try. Any idea why I can successfully run PRSice with UKB bgen data (400K samples) but I’m unable to my small study of (300 samples)? If PRSice could handle the memory for UKB I would think it should handle for a smaller set?

It seems that however you allocate the memory, it is not allocating properly for my study data? Any thoughts?

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 4:32 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author author@noreply.github.com Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

Sam

On Wed, Feb 17, 2021 at 5:29 PM batzler notifications@github.com<mailto:notifications@github.com> wrote:

Additionally, I've successfully used the UKB bgen files to run PRSice. So its the creation of bgen files from the Michigan imputation server VCF's that is presenting a problem. Thanks, Tony

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/257#issuecomment-780896789, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYTM6RQIWA355Z5DGSLS7Q7LPANCNFSM4XZFSKTA .

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choishingwan commented 3 years ago

the --memory option is really just there for permutation. It doesn't work for other stuff. Can you confirm if you can run the QCTools on your small bgen samples? Currently PRSice only support BGEN v1.1. and v1.2, so if your bgen file is v1.3, then PRSice might crash. There are also many other reason that might be happening here, but since 2.2.10 is rather old, it'd be very hard for me to figure that out.

Sam

batzler commented 3 years ago

I’m using plink2 to export bgen-1.2

I just got this to run for chr22 successfully.

The problem occurs when I try to run more than that.

If I provide the chroms 1-22 base data (8 million variant results), and provide the chr# bgen target data, it fails due to memory. If I provide the chroms 1-22 base data, but I only provide chr22 bgen target data (83,000 variants), it fails due to memory. If I subset the base data to chr22 (100,000 variant results) , and provide chr22 bgen target data (83,000 variants) only, it finishes properly.

Any explanation of why this might happen?

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 4:40 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author author@noreply.github.com Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

Sam

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choishingwan commented 3 years ago

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

batzler commented 3 years ago

No problem. This is very helpful to know. Will try the new version and keep you posted. Thanks Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author author@noreply.github.com Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/choishingwan/PRSice/issues/257#issuecomment-780911196, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AS4PKZXZIQUONHTTZIKMGRLS7RDFDANCNFSM4XZFSKTA.

batzler commented 3 years ago

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/choishingwan/PRSice/issues/257#issuecomment-780911196, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AS4PKZXZIQUONHTTZIKMGRLS7RDFDANCNFSM4XZFSKTA.

choishingwan commented 3 years ago

you don't have write permission to the out file directory

On Mon, Feb 22, 2021 at 5:09 PM batzler notifications@github.com wrote:

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author < author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/choishingwan/PRSice/issues/257#issuecomment-780911196>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AS4PKZXZIQUONHTTZIKMGRLS7RDFDANCNFSM4XZFSKTA>.

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batzler commented 3 years ago

Forgive me if I’m misunderstanding, but the OUTDIR that I’m attempting to write, does not have permission issues. I even tried chmod 777 and still received the error below. Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:12 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author author@noreply.github.com Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

you don't have write permission to the out file directory

On Mon, Feb 22, 2021 at 5:09 PM batzler notifications@github.com<mailto:notifications@github.com> wrote:

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice PRSice@noreply.github.com<mailto:PRSice@noreply.github.com> Cc: Batzler, Anthony Batzler.Anthony@mayo.edu<mailto:Batzler.Anthony@mayo.edu>; Author < author@noreply.github.commailto:author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/choishingwan/PRSice/issues/257#issuecomment-780911196>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AS4PKZXZIQUONHTTZIKMGRLS7RDFDANCNFSM4XZFSKTA>.

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choishingwan commented 3 years ago

That error occurs when PRSice failed to write the log file into the designated output directory. Can you run PRSice with just PRSice --version or PRSice --help? If so then it is very likely due to the permission / disk quota problem as those are the two commands that doesn't require file write access.

Sam

On Mon, Feb 22, 2021 at 5:16 PM batzler notifications@github.com wrote:

Forgive me if I’m misunderstanding, but the OUTDIR that I’m attempting to write, does not have permission issues. I even tried chmod 777 and still received the error below. Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:12 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author < author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

you don't have write permission to the out file directory

On Mon, Feb 22, 2021 at 5:09 PM batzler <notifications@github.com<mailto: notifications@github.com>> wrote:

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice <PRSice@noreply.github.com<mailto: PRSice@noreply.github.com>> Cc: Batzler, Anthony <Batzler.Anthony@mayo.edu<mailto: Batzler.Anthony@mayo.edu>>; Author < author@noreply.github.commailto:author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/choishingwan/PRSice/issues/257#issuecomment-780911196>,

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.

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batzler commented 3 years ago

Here is version

batzler@mforgehn2 GWAS12merged.EUR.lindner_EUR.00001.MAF0.05.dosR20.8]$ /research/bsi/tools/biotools/prsice/2.3.3/PRSice_linux --version 2.3.3 (2020-08-05)

Here is help (abbreviated)

[batzler@mforgehn2 GWAS12merged.EUR.lindner_EUR.00001.MAF0.05.dosR20.8]$ /research/bsi/tools/biotools/prsice/2.3.3/PRSice_linux --help usage: PRSice [options] <-b base_file> <-t target_file>

Base File: --a1 Column header containing allele 1 (effective allele) Default: A1 --a2 Column header containing allele 2 (non-effective allele)

I’m calling PRSice with the following

${R} ${PRSice}/PRSice.R \ --prsice ${PRSice}/PRSice_linux \

I’m assuming this is still appropriate as this is how we called the old version of PRSice. Also, my output and current directories both have plenty of space available…

Any other thoughts? I can discuss with our IT as well. Not sure if this is an install issue on their end…?

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:19 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author author@noreply.github.com Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

Sam

On Mon, Feb 22, 2021 at 5:16 PM batzler notifications@github.com<mailto:notifications@github.com> wrote:

Forgive me if I’m misunderstanding, but the OUTDIR that I’m attempting to write, does not have permission issues. I even tried chmod 777 and still received the error below. Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:12 PM To: choishingwan/PRSice PRSice@noreply.github.com<mailto:PRSice@noreply.github.com> Cc: Batzler, Anthony Batzler.Anthony@mayo.edu<mailto:Batzler.Anthony@mayo.edu>; Author < author@noreply.github.commailto:author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

you don't have write permission to the out file directory

On Mon, Feb 22, 2021 at 5:09 PM batzler <notifications@github.com<mailto: mailto:notifications@github.com%3cmailto:%0b> notifications@github.commailto:notifications@github.com>> wrote:

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice <PRSice@noreply.github.com<mailto: mailto:PRSice@noreply.github.com%3cmailto:%0b> PRSice@noreply.github.commailto:PRSice@noreply.github.com>> Cc: Batzler, Anthony <Batzler.Anthony@mayo.edu<mailto: mailto:Batzler.Anthony@mayo.edu%3cmailto:%0b> Batzler.Anthony@mayo.edumailto:Batzler.Anthony@mayo.edu>>; Author < author@noreply.github.commailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/choishingwan/PRSice/issues/257#issuecomment-780911196>,

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choishingwan commented 3 years ago

If you do --out /

does that work?

On Mon, Feb 22, 2021 at 5:25 PM batzler notifications@github.com wrote:

Here is version

batzler@mforgehn2 GWAS12merged.EUR.lindner_EUR.00001.MAF0.05.dosR20.8]$ /research/bsi/tools/biotools/prsice/2.3.3/PRSice_linux --version 2.3.3 (2020-08-05)

Here is help (abbreviated)

[batzler@mforgehn2 GWAS12merged.EUR.lindner_EUR.00001.MAF0.05.dosR20.8]$ /research/bsi/tools/biotools/prsice/2.3.3/PRSice_linux --help usage: PRSice [options] <-b base_file> <-t target_file>

Base File: --a1 Column header containing allele 1 (effective allele) Default: A1 --a2 Column header containing allele 2 (non-effective allele)

I’m calling PRSice with the following

${R} ${PRSice}/PRSice.R \ --prsice ${PRSice}/PRSice_linux \

I’m assuming this is still appropriate as this is how we called the old version of PRSice. Also, my output and current directories both have plenty of space available…

Any other thoughts? I can discuss with our IT as well. Not sure if this is an install issue on their end…?

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:19 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author < author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

That error occurs when PRSice failed to write the log file into the designated output directory. Can you run PRSice with just PRSice --version or PRSice --help? If so then it is very likely due to the permission / disk quota problem as those are the two commands that doesn't require file write access.

Sam

On Mon, Feb 22, 2021 at 5:16 PM batzler <notifications@github.com<mailto: notifications@github.com>> wrote:

Forgive me if I’m misunderstanding, but the OUTDIR that I’m attempting to write, does not have permission issues. I even tried chmod 777 and still received the error below. Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:12 PM To: choishingwan/PRSice <PRSice@noreply.github.com<mailto: PRSice@noreply.github.com>> Cc: Batzler, Anthony <Batzler.Anthony@mayo.edu<mailto: Batzler.Anthony@mayo.edu>>; Author < author@noreply.github.commailto:author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

you don't have write permission to the out file directory

On Mon, Feb 22, 2021 at 5:09 PM batzler <notifications@github.com <mailto: mailto:notifications@github.com%3cmailto:%0b> notifications@github.com mailto:notifications@github.com>> wrote:

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice <PRSice@noreply.github.com<mailto: mailto:PRSice@noreply.github.com%3cmailto:%0b> PRSice@noreply.github.com mailto:PRSice@noreply.github.com>> Cc: Batzler, Anthony <Batzler.Anthony@mayo.edu<mailto: mailto:Batzler.Anthony@mayo.edu%3cmailto:%0b> Batzler.Anthony@mayo.edu mailto:Batzler.Anthony@mayo.edu>>; Author < author@noreply.github.com<mailto:author@noreply.github.com<mailto: author@noreply.github.com%3cmailto:author@noreply.github.com>>> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

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batzler commented 3 years ago

Seems there is some issue with the script writing to a different location other than the current directory from which I’m running. Some kind of permissions issue. Even though the –out dir is open for write access. I can work around this. Thanks for the suggestions. Seems to be working now. Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:38 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author author@noreply.github.com Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

If you do --out /

does that work?

On Mon, Feb 22, 2021 at 5:25 PM batzler notifications@github.com wrote:

Here is version

batzler@mforgehn2 GWAS12merged.EUR.lindner_EUR.00001.MAF0.05.dosR20.8]$ /research/bsi/tools/biotools/prsice/2.3.3/PRSice_linux --version 2.3.3 (2020-08-05)

Here is help (abbreviated)

[batzler@mforgehn2 GWAS12merged.EUR.lindner_EUR.00001.MAF0.05.dosR20.8]$ /research/bsi/tools/biotools/prsice/2.3.3/PRSice_linux --help usage: PRSice [options] <-b base_file> <-t target_file>

Base File: --a1 Column header containing allele 1 (effective allele) Default: A1 --a2 Column header containing allele 2 (non-effective allele)

I’m calling PRSice with the following

${R} ${PRSice}/PRSice.R \ --prsice ${PRSice}/PRSice_linux \

I’m assuming this is still appropriate as this is how we called the old version of PRSice. Also, my output and current directories both have plenty of space available…

Any other thoughts? I can discuss with our IT as well. Not sure if this is an install issue on their end…?

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:19 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Batzler, Anthony Batzler.Anthony@mayo.edu; Author < author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

That error occurs when PRSice failed to write the log file into the designated output directory. Can you run PRSice with just PRSice --version or PRSice --help? If so then it is very likely due to the permission / disk quota problem as those are the two commands that doesn't require file write access.

Sam

On Mon, Feb 22, 2021 at 5:16 PM batzler <notifications@github.com<mailto: notifications@github.com>> wrote:

Forgive me if I’m misunderstanding, but the OUTDIR that I’m attempting to write, does not have permission issues. I even tried chmod 777 and still received the error below. Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Monday, February 22, 2021 4:12 PM To: choishingwan/PRSice <PRSice@noreply.github.com<mailto: PRSice@noreply.github.com>> Cc: Batzler, Anthony <Batzler.Anthony@mayo.edu<mailto: Batzler.Anthony@mayo.edu>>; Author < author@noreply.github.commailto:author@noreply.github.com> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

you don't have write permission to the out file directory

On Mon, Feb 22, 2021 at 5:09 PM batzler <notifications@github.com <mailto: mailto:notifications@github.com%3cmailto:%0b> notifications@github.com mailto:notifications@github.com>> wrote:

Sam, Thanks again for suggestions to use the new version. I had our IT dept install the new version and I’m trying out now. I’ve got all of my data setup and everything looks to be correct however I’m running into this error when trying to execute PRSice. Any thoughts here?

Error: Reporter not initialized! Error: Execution halted

Thanks, Tony

From: Shing Wan Choi [mailto:notifications@github.com] Sent: Wednesday, February 17, 2021 5:02 PM To: choishingwan/PRSice <PRSice@noreply.github.com<mailto: mailto:PRSice@noreply.github.com%3cmailto:%0b> PRSice@noreply.github.com mailto:PRSice@noreply.github.com>> Cc: Batzler, Anthony <Batzler.Anthony@mayo.edu<mailto: mailto:Batzler.Anthony@mayo.edu%3cmailto:%0b> Batzler.Anthony@mayo.edu mailto:Batzler.Anthony@mayo.edu>>; Author < author@noreply.github.com<mailto:author@noreply.github.com<mailto: author@noreply.github.com%3cmailto:author@noreply.github.com>>> Subject: [EXTERNAL] Re: [choishingwan/PRSice] Issue with bgen vs bed (#257)

It might be related to an old bug related to multiple chromosome input. Again, I am uncertain because 2.2.10 is more than a year ago... Sorry about that .

Sam

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stale[bot] commented 3 years ago

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