malformed tbi file

[smhaider]

Hi,

I just wanted to point out an error while running epacts-groups with the latest commit "e4dfca2d79a4c559e654d7bce52bc422b471f923" it works fine with single variant test whereas if I use the same vcf with epacts-groups skat-o I run into an error "malformed tbi index". Secondly I have tested the same vcf and tbi file with epact version 3.3.2 commit id "a5209db1b3929c4dd2f15f27ea085edf3a634ee7" it works fine.

Regards,
Haider

[smhaider]

just for information here is the recipe I am using to build the container.

recipeEPACTS.txt

[jonathonl]

How was the tbi index generated? Can you share the tbi file?

[smhaider]

Hi, Thanks for your kind response. I used tabix -pvcf input.vcf.gz. I have already tried compressing and indexing the vcf file multiple times and got the same error. Please find the indexed file in the attachment. Just for your reference I have also attached recipes I used to build both versions. This same vcf and index file works with v3.3.2 but not with version 3.4.2. lastly, just for your reference although there has been many updates in the requirement.txt file but at the moment none of the update works since the zlib path has been changed, so as you can see in the recipe of 3.4.2, we have to use a different way to install "statgen/savvy" Thanks again for your kind response, looking forward to hearing from you. Kind Regards, Haider

[jonathonl]

Haider, I don't see the attachment.

[smhaider]

Hi,

sorry for the inconvenience I replied directly via email which somehow messed up the attachment. anyhow since github does not allow me to upload tbi file I have put everything in a compressed folder. it contains recipe used to build both versions and the tbi file.

thanks again for your reply.

Regards
Data.zip

[jonathonl]

Thanks I just pushed a fix for this to statgen/savvy. Please run the following and then give it another try:

cget remove statgen/savvy --yes
cget install statgen/savvy@9ba1ab13e8afdbd09d4ae63bdf9fd0ac63229f99
cd build && make clean && make

[smhaider]

Hi, Thanks for your quick response, just to confirm if I understood it correctly, I should replace this part of my recipe “ cget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" statgen/savvy mkdir build; cd build cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DCMAKE_BUILD_TYPE=Release .. make make install” with “ cget remove statgen/savvy --yes cget install ***@***.*** cd build && make clean && make” and rebuild the container? And just one last question, emmaxCMC is not able to handle sample size greater then 47000 just curious if this will be fixed any time soon?

[jonathonl]

Since your container is always building with the latest from savvy, you could just rebuild the container image without modifying the definition file.  - JLOn Feb 24, 2023, at 15:40, smhaider ***@***.***> wrote: Hi, Thanks for your quick response, just to confirm if I understood it correctly, I should replace this part of my recipe “ cget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" statgen/savvy mkdir build; cd build cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DCMAKE_BUILD_TYPE=Release .. make make install” with “ cget remove statgen/savvy --yes cget install ***@***.*** cd build && make clean && make” and rebuild the container? And just one last question, emmaxCMC is not able to handle sample size greater then 47000 just curious if this will be fixed any time soon?

On Fri 24. Feb 2023 at 21:20, Jonathon LeFaive ***@***.***> wrote: Thanks I just pushed a fix for this to statgen/savvy. Please run the following and then give it another try: cget remove statgen/savvy --yes cget install ***@***.*** cd build && make clean && make — Reply to this email directly, view it on GitHub <#48 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEN3KT3S7BXYH2HXBEL6RWTWZEJZ7ANCNFSM6AAAAAAVFOMOBE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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----------------------------------------------- Syed M. Ijlal Haider, MSc. PhD, Department of Bioinformatics Universität zu Lübeck Haus 67/ BMF 1.OG, R.32 Ratzeburger Allee 160 23562 Lübeck Tel.: +49 451 3101 8324 —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>

[smhaider]

Perfect. Thanks again for your help, I will test it tomorrow and will let you know. Have a great weekend.

[smhaider]

Hi, Just to let you know that I have tried again and it works fine now. thanks again for your help

Have a great weekend

[smhaider]

Hi sorry for bothering you again, I just wanted to bring into your notice that I think the --min-callrate 0.95 filter is not working in epacts-group. probably this is the reason why I got different results from same tests in between EPACTS and Raremetal.