No output detected

[Nik Tz]

Hello,

I'm trying to pmerge some files, but getting the warning 'No output detected. Exiting'. I've tried running it with  --make-pgen and  --make-bed with same error.

What do I need to change please?

plink2 \
           --pfile \"${pgen_path}wes_pgen_12a\"
           --pmerge \
           \"${pgen_path}wes_pgen_12b.pgen\" \
           \"${pgen_path}wes_pgen_12b.pvar\" \
           \"${pgen_path}wes_pgen_12b.psam\" \
           --make-bed \
           --out wes_merged_12

Many thanks, Nik

[Nik Tz]

To clarify, wes_pgen_12a refers to a set of plink files (.pgen, .pvar, .psam).

I have removed some of the backslashes in case those were confusing the program, and now have:

plink2 --pfile "${pgen_path}wes_pgen_12a" \
       --pmerge "${pgen_path}wes_pgen_12b.pgen" \
               "${pgen_path}wes_pgen_12b.pvar" \
               "${pgen_path}wes_pgen_12b.psam" \
       --make-bed \
       --out wes_merged_12

However, I'm now getting the following log:

--pmerge: 939608 samples present.
--pmerge: Merged .psam written to wes_merged_12.psam .
--pmerge: 2 .pvar files scanned.

Error: Non-concatenating --pmerge-list is under development.
Error: Failed to open wes_merged_12.pgen : No such file or directory.

When trying to --make-pgen, I run into similar issues:

plink2 --pfile "${pgen_path}wes_pgen_12a" \
       --pmerge "${pgen_path}wes_pgen_12b.pgen" \
               "${pgen_path}wes_pgen_12b.pvar" \
               "${pgen_path}wes_pgen_12b.psam" \

       --make-pgen \
       --out wes_merged_12

--pmerge: 939608 samples present.
--pmerge: Merged .psam written to wes_merged_12-merge.psam .
--pmerge: 2 .pvar files scanned.

Error: Non-concatenating --pmerge-list is under development.
Error: Failed to open wes_merged_12-merge.pgen : No such file or directory.

This seems to me a simple case of merging so I don't understand the first error re concatenation, 

and I'm not sure why it's flagging up an error in accessing one of the output files?

Grateful for your thoughts, thank you

[Christopher Chang]

You must be using an old plink2 build where I forgot to make plink2 finish erroring out properly after printing the "Non-concatenating --pmerge-list is under development" message.

The current workaround for this missing functionality is to export to BCF, use "bcftools merge" to perform the merge, and then use --bcf to import the result.  Note that if you have dosage data and want to keep it, you need to include "vcf-dosage=DS" in your export command and "dosage=DS" in your re-import command.

[Nik Tz]

That's great thanks so much for your time, Chris, I'll try this. The version is PLINK v2.00a3.1LM 64-bit Intel (19 May 2022) but it's via UK Biobank so I think stuck with this...