filenameXYZ.bim could not be scanned twice, plink2
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Summaira Yasmeen
Jul 20, 2023, 6:45:53 AM7/20/23
to plink2-users
Hi Chris,
I am using PLINK2 to merge heavy files (binary filesets) and then exporting them into bgen format. One of the file caused problem, if i remove that file - merging works.
I tried to investigate whether it is problem with that specific input fileset, but if i only attempt exporting that input fileset to bgen format- it works. However, if that fileset is part in merge list, it throws following error:
PLINK v2.00a3.1LM 64-bit Intel (19 May 2022) www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to chr16merged.log.
Options in effect:
--delete-pmerge-result
--export bgen-1.2 bits=8 ref-first
--out chr16merged
--pmerge-list chr16.binaryfileset
--pmerge-output-vzs
Start time: xxxxxxxxxx
257911 MiB RAM detected; reserving 128955 MiB for main workspace.
Using up to 64 threads (change this with --threads).
--pmerge-list: 47 filesets specified.
--pmerge-list: xxxxxxxx samples and xxx phenotype present.
--pmerge-list: Merged .psam written to chr16merged.psam .
--pmerge-list: 47 .pvar files scanned.
Concatenation job detected.
Error: filenameXYZ.bim could not be scanned twice.
Concatenating... 0/1262610 variants complete.
End time: xxxxxxxxx
I am using PLINK2 to merge heavy files (binary filesets) and then exporting them into bgen format. One of the file caused problem, if i remove that file - merging works.
I tried to investigate whether it is problem with that specific input fileset, but if i only attempt exporting that input fileset to bgen format- it works. However, if that fileset is part in merge list, it throws following error:
' filenameXYZ.bim could not be scanned twice'
logfile:
plink2 --pmerge-list chr16.binaryfileset --pmerge-output-vzs --export bgen-1.2 bits=8 ref-first --delete-pmerge-result --out chr16merged
PLINK v2.00a3.1LM 64-bit Intel (19 May 2022) www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to chr16merged.log.
Options in effect:
--delete-pmerge-result
--export bgen-1.2 bits=8 ref-first
--out chr16merged
--pmerge-list chr16.binaryfileset
--pmerge-output-vzs
Start time: xxxxxxxxxx
257911 MiB RAM detected; reserving 128955 MiB for main workspace.
Using up to 64 threads (change this with --threads).
--pmerge-list: 47 filesets specified.
--pmerge-list: xxxxxxxx samples and xxx phenotype present.
--pmerge-list: Merged .psam written to chr16merged.psam .
--pmerge-list: 47 .pvar files scanned.
Concatenation job detected.
Error: filenameXYZ.bim could not be scanned twice.
Concatenating... 0/1262610 variants complete.
Concatenating... 10000/1262610 variants complete.
Concatenating... 20000/1262610 variants complete.
Concatenating... 30000/1262610 variants complete.
Concatenating... 40000/1262610 variants complete.
Concatenating... 50000/1262610 variants complete.
Concatenating... 60000/1262610 variants complete.
(Process-substitution/named-pipe input is not permitted in this use case.)
Concatenating... 20000/1262610 variants complete.
Concatenating... 30000/1262610 variants complete.
Concatenating... 40000/1262610 variants complete.
Concatenating... 50000/1262610 variants complete.
Concatenating... 60000/1262610 variants complete.
(Process-substitution/named-pipe input is not permitted in this use case.)
End time: xxxxxxxxx
Looking forward to the support,
Summaira
Summaira
Christopher Chang
Jul 21, 2023, 12:05:04 PM7/21/23
to plink2-users
The Recent version history shows a --pmerge-list bugfix after May 2022, so you should retry this run with a newer build.
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