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JonJala
Could not open /usr/local/bin/ld_ref_panel/eur_w_ld_chr/1.l2.ldscore[./gz/bz2]
I'm trying to run MTAG with default options and I'm getting following error:
Could not open /usr/local/bin/ld_ref_panel/eur_w_ld_chr/1.l2.ldscore[./gz/bz2]
How can I address this issue?
TIA
Hello,
Can you attach the complete log file? Hard to debug without it.
Patrick
On Tue, Apr 5, 2022 at 7:18 AM Mahantesh Biradar @.***> wrote:
I'm trying to run MTAG with default options and I'm getting following error:
Could not open /usr/local/bin/ld_ref_panel/eur_w_ld_chr/1.l2.ldscore[./gz/bz2]
How can I address this issue?
TIA
— Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/156, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5K7HANTFA52JCSDCYTVDQORTANCNFSM5SSNEKDA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
The log file would help, though that error seems a little weird. How are you trying to run MTAG? It looks like you maybe have the mtag.py file sitting in /usr/local/bin? It's meant to be run out of a clone of the repo, and should therefore file the eur_w_ld_chr directory in the same place.
I suppose you could pass the path to LD panel using "--ld_ref_panel" so it won't try to look in what it expects to be a repo, and that should hopefully move you further along, though if you're running this in a non-standard way, there are no guarantees you won't run into other issues.
Thanks for your suggestion. I sorted this out by including following command in my code:
--ld_ref_panel /opt/MTAG/mtag/mtag/ld_ref_panel/eur_w_ld_chr/ \
However, now I have a new error, which I didn't face before.
Hi,
It's hard to diagnose this problem without the full log file. Are you able to share it?
Patrick
On Tue, Apr 5, 2022 at 10:59 AM Mahantesh Biradar @.***> wrote:
Thanks for your suggestion. I sorted this out by including following command in my code:
--ld_ref_panel /opt/MTAG/mtag/mtag/ld_ref_panel/eur_w_ld_chr/ \
However, now I have a new error, which I didn't face before. [image: Error-New] https://user-images.githubusercontent.com/7866207/161783568-ae228552-fec4-446e-91c2-5238574d4c1d.JPG
— Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/156#issuecomment-1088824345, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5KQHACQL3NDIPKO2Q3VDRIMPANCNFSM5SSNEKDA . You are receiving this because you commented.Message ID: @.***>
Hi Patrick - I have sent you an email. Please let me know if you need more details. Thanks in advance.
Hi Mahantesh,
I received your email, but you've only sent a few lines of the log file from your run, so It is difficult to diagnose what is wrong. Are you able to share the complete log file?
Best, Patrick
On Tue, Apr 5, 2022 at 2:50 PM Mahantesh Biradar @.***> wrote:
Hi Patrick - I have sent you an email. Please let me know if you need more details. Thanks in advance.
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It appears to be breaking down on the step when the associations are divided by maf*(1-maf), so my best guess is that some of the SNPs have an allele frequency of zero or one or maybe the frequency is missing. Can you verify whether you have non-missing allele frequencies for every SNP in each file and that they are strictly between zero and one? Even better if they are between .01 and .99.
On Wed, Apr 6, 2022 at 9:40 AM Mahantesh Biradar @.***> wrote:
Hi Patrick, I have emailed you the complete log.
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