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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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KING ERROR: Segmentation fault (core dumped) (return code 139). #107

Closed freedomq8 closed 5 years ago

freedomq8 commented 5 years ago

Hello,

I am getting this error when trying to execute KING command on vtools 2.7.0 for Python 2.7.12 on mac laptop. I thought I came across this problem before but not sure how did I solve it but I am sure its either using different machine or different versions of KING and/or plink.

INFO: Executing KING.king_0: Load specified snapshot if a snapshot is specified. Otherwise use the existing project.
INFO: Executing KING.king_10: Check the existence of KING and PLINK command.
INFO: Command /home/tutankhmun/soft/king is located.
INFO: Command /home/tutankhmun/soft/plink is located.
INFO: Executing KING.king_20: Write selected variant and samples in tped format
INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.tped
INFO: Executing KING.king_21: Rename tfam file to match tped file
INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.tfam
INFO: Executing KING.king_30: Calculate LD pruning candidate list with a cutoff of R^2=0.5
INFO: Running /home/tutankhmun/soft/plink --noweb --tped KING.tped --tfam KING.tfam --indep-pairwise 50 5 0.5 --allow-no-sex --out KING.LD.50 under /mnt/c/diabetes/.vtools_cache
ERROR: Segmentation fault (core dumped)
ERROR:
ERROR: Failed to execute step king_30: Execution of command '/home/tutankhmun/soft/plink --noweb --tped KING.tped --tfam KING.tfam --indep-pairwise 50 5 0.5 --allow-no-sex --out KING.LD.50' failed after 00:00:00 (return code 139).

any suggestions? thanks

freedomq8 commented 5 years ago

Hello again, i ran KING on vtools.2.70 for Python 2.7.12 on PC and got another error. is this king specific issue or vtools ?

INFO: Executing KING.king_0: Load specified snapshot if a snapshot is specified. Otherwise use the existing project. INFO: Executing KING.king_10: Check the existence of KING and PLINK command. INFO: Command /home/daruma/soft/king is located. INFO: Command /home/daruma/soft/plink is located. INFO: Executing KING.king_20: Write selected variant and samples in tped format WARNING: Size of existing file differ from recorded file: diabetes.proj INFO: Running vtools export rare_nonsyn_vars --format tped --samples "1" | awk '{$2=$1"_"$4;$3=0;print $0}' > cache/KING.tped INFO: Executing KING.king_21: Rename tfam file to match tped file INFO: Running mv rare_nonsyn_vars.tfam cache/KING.tfam ERROR: mv: symbol lookup error: mv: undefined symbol: mode_to_security_class ERROR: ERROR: Failed to execute step king_21: Execution of command 'mv rare_nonsyn_vars.tfam cache/KING.tfam' failed after 00:00:00 (return code 127).

any suggestion ?

thanks

BoPeng commented 5 years ago

Can you try to run the command manually

/home/tutankhmun/soft/plink --noweb --tped KING.tped --tfam KING.tfam --indep-pairwise 50 5 0.5 --allow-no-sex --out KING.LD.50

and see if all input files are there and what error messages it gives?

freedomq8 commented 5 years ago

/home/tutankhmun/soft/plink --noweb --tped KING.tped --tfam KING.tfam --indep-pairwise 50 5 0.5 --allow-no-sex --out KING.LD.50 ​ @----------------------------------------------------------@​ | PLINK! | v1.07 | 10/Aug/2009 |​ |----------------------------------------------------------|​ | (C) 2009 Shaun Purcell, GNU General Public License, v2 |​ |----------------------------------------------------------|​ | For documentation, citation & bug-report instructions: |​ | http://pngu.mgh.harvard.edu/purcell/plink/ |​ @----------------------------------------------------------@​ ​ Segmentation fault (core dumped)

this is the error I got

From: Bo notifications@github.com Sent: Wednesday, June 12, 2019 11:36 PM To: vatlab/VariantTools Cc: freedomq8; Author Subject: Re: [vatlab/VariantTools] KING ERROR: Segmentation fault (core dumped) (return code 139). (#107)

Can you try to run the command manually

/home/tutankhmun/soft/plink --noweb --tped KING.tped --tfam KING.tfam --indep-pairwise 50 5 0.5 --allow-no-sex --out KING.LD.50

and see if all input files are there and what error messages it gives?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/vatlab/VariantTools/issues/107?email_source=notifications&email_token=AKAVSMXCBU3ONRBPKJS3YJDP2FM3BA5CNFSM4HW3NORKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXRXG2Y#issuecomment-501445483, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKAVSMS762BJVTYDNTHVXRLP2FM3BANCNFSM4HW3NORA.

BoPeng commented 5 years ago

Then perhaps you can install a different version of plink and/or run plink on other files to check it is properly installed? seqfault could be installation problem, or because invalid input file, in which case you should manually check the input files.

freedomq8 commented 5 years ago

I tried different versions of plink but still the same error. it could be OS issue as for this machine I am using ubuntu on windows. someone mentioned having the same issue on ubuntu on windows with plink

https://groups.google.com/forum/#!topic/plink2-users/m051Ez2MJdM [http://www.google.com/images/icons/product/groups-128.png]https://groups.google.com/forum/#!topic/plink2-users/m051Ez2MJdM Segmentation fault (core dumped),https://groups.google.com/forum/#!topic/plink2-users/m051Ez2MJdM Posted 3/8/18 9:49 PM, 6 messages groups.google.com

however I am having another error with KING on ubuntu by its own with error code 127

(base) daruma@daruma:/media/daruma/sea8/diabetic$ vtools execute KING --var_table rare_nonsyn_vars --king_path=/home/daruma/soft --plink_path=/home/daruma/soft INFO: Executing KING.king_0: Load specified snapshot if a snapshot is specified. Otherwise use the existing project.​ INFO: Executing KING.king_10: Check the existence of KING and PLINK command.​ INFO: Command /home/daruma/soft/king is located.​ INFO: Command /home/daruma/soft/plink is located.​ INFO: Executing KING.king_20: Write selected variant and samples in tped format​ INFO: Reuse existing cache/KING.tped​ INFO: Executing KING.king_21: Rename tfam file to match tped file​ INFO: Running mv rare_nonsyn_vars.tfam cache/KING.tfam​ ERROR: mv: symbol lookup error: mv: undefined symbol: mode_to_security_class​ ERROR: ​ ERROR: Failed to execute step king_21: Execution of command 'mv rare_nonsyn_vars.tfam cache/KING.tfam' failed after 00:00:00 (return code 127).​ ​ ​

From: Bo notifications@github.com Sent: Wednesday, June 12, 2019 11:50 PM To: vatlab/VariantTools Cc: freedomq8; Author Subject: Re: [vatlab/VariantTools] KING ERROR: Segmentation fault (core dumped) (return code 139). (#107)

Then perhaps you can install a different version of plink and/or run plink on other files to check it is properly installed? seqfault could be installation problem, or because invalid input file, in which case you should manually check the input files.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/vatlab/VariantTools/issues/107?email_source=notifications&email_token=AKAVSMUVAMTF3OY3DF2WYWTP2FOS7A5CNFSM4HW3NORKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXRYM4Q#issuecomment-501450354, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKAVSMQDPHJHVN4YVMILU53P2FOS7ANCNFSM4HW3NORA.

freedomq8 commented 5 years ago

hello,

I manage to solve code 139 by using another plink version from this source http://s3.amazonaws.com/plink1-assets/dev/plink_linux_x86_64.zip

then I got another 127 that I manage to manually move/rename the file to cache directory and delete king21 step from KING.pipeline

but now I am getting code 1 error

vtools execute KING --var_table rare_nonsyn_vars --king_path=/home/tutankhmun/soft --plink_path=/home/tutankhmun/soft INFO: Executing KING.king_0: Load specified snapshot if a snapshot is specified. Otherwise use the existing project. INFO: Executing KING.king_10: Check the existence of KING and PLINK command. INFO: Command /home/tutankhmun/soft/king is located. INFO: Command /home/tutankhmun/soft/plink is located. INFO: Executing KING.king_20: Write selected variant and samples in tped format INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.tped INFO: Executing KING.king_21: Rename tfam file to match tped file INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.tfam INFO: Executing KING.king_30: Calculate LD pruning candidate list with a cutoff of R^2=0.5 INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.LD.50.prune.in INFO: Executing KING.king_31: LD pruning from pre-calculated list INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.bed INFO: Executing KING.king_41: Global ancestry inference INFO: Running /home/tutankhmun/soft/king -b KING.bed --mds --ibs --prefix KING- under /mnt/c/diabetes/.vtools_cache ERROR: ERROR: Failed to execute step king_41: Execution of command '/home/tutankhmun/soft/king -b KING.bed --mds --ibs --prefix KING-' failed after 00:00:00 (return code 1). tutankhmun@daruma:/mnt/c/diabetes$ sudo vtools execute KING --var_table rare_nonsyn_vars --king_path=/home/tutankhmun/soft --plink_path=/home/tutankhmun/soft INFO: Executing KING.king_0: Load specified snapshot if a snapshot is specified. Otherwise use the existing project. INFO: Executing KING.king_10: Check the existence of KING and PLINK command. INFO: Command /home/tutankhmun/soft/king is located. INFO: Command /home/tutankhmun/soft/plink is located. INFO: Executing KING.king_20: Write selected variant and samples in tped format INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.tped INFO: Executing KING.king_21: Rename tfam file to match tped file INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.tfam INFO: Executing KING.king_30: Calculate LD pruning candidate list with a cutoff of R^2=0.5 INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.LD.50.prune.in INFO: Executing KING.king_31: LD pruning from pre-calculated list INFO: Reuse existing /mnt/c/diabetes/.vtools_cache/KING.bed INFO: Executing KING.king_41: Global ancestry inference INFO: Running /home/tutankhmun/soft/king -b KING.bed --mds --ibs --prefix KING- under /mnt/c/diabetes/.vtools_cache ERROR: ERROR: Failed to execute step king_41: Execution of command '/home/tutankhmun/soft/king -b KING.bed --mds --ibs --prefix KING-' failed after 00:00:00 (return code 1).

i am not sure if its OS error or installing issue. is there a VM with vtools installed or docker of vtools ?