PLINK 1.9 make-bed only produces '-temporary' files with no explanatory error message

Question

[vlindsay18]

I'm trying to turn a tped & tfam file to bfile format using PLINK 1.9.

My tped is set out like this:

1   AX-XXX   0   1000   A   T   A   A

My tfam something like this:

F1   001   0   0   1   1

I ran:

plink --tfile INPUT --autosome-num 31 --allow-extra-chr --keep-allele-order --debug --make-bed --out OUTPUT

And the output I get is just an OUTPUT-temporary.bed .bim and .fam file. I've run the --debug flag, and the log I get is as so:

Processing .tped file.
OUTPUT-temporary.bed + OUTPUT-temporary.bim + OUTPUT-temporary.fam written.

And everything stops there. I've tried increasing the memory (it reserved 257785 MB in my last run), I've made sure all missing calls are set to 0, but I get no actual error message at all so it's really hard to know whether it's an issue with my files or the commands I'm using or something else.

I also tried --recode and --recode vcd just to see if this issue happened with other commands, and the same thing happens.

Any ideas much appreciated.

Answer 1

[chrchang523]

Can you post the full .log/console output, including the version string?

[vlindsay18]

Yes:

PLINK v1.90b6.16 64-bit (19 Feb 2020)
Options in effect:
--allow-extra-chr
--autosome-num 31
--debug
--make-bed
--out array_import
--tfile array_data_raw

Hostname: [redacted]
Working directory: [redacted]
Start time: Tue Apr 28 14:02:45 2020

Random number seed: 1588082565
515571 MB RAM detected; reserving 257785 MB for main workspace.
Processing .tped file.
array_import-temporary.bed + array_import-temporary.bim + array_import-temporary.fam written.

And that is all I get.

Edit: I have successfully imported a VCF from another dataset to PLINK binary format in the last few days with this same version, so I feel like it's probably an issue with the tfiles, but I had some others from my group look them over and no one can spot an obvious issue with them.

[chrchang523]

I'm unable to replicate this issue. Is it possible for you to send me a .tped+.tfam which triggers this behavior? If not, I can send you a series of debug builds to try to nail down what's happening, but that process may take much longer.

[vlindsay18]

Let me check whether I have permission to forward the data on - I'll get right back to you.

[vlindsay18]

Yes, I can send you this on. What is the best email? Thanks for your help with this!

[chrchang523]

[my username] at gmail

[vlindsay18]

Thank you, much appreciated!

[chrchang523]

This is definitely a plink bug (a segfault occurred), working on a fix now.

[chrchang523]

Bugfix is now posted. This will now print a regular error message on your data; you need to use --chr-set (which permits chrY) instead of --autosome-num.

[vlindsay18]

That's amazing - thank you very much!

Answer 2

[gimeno]

Hello @chrchang523 I tried to read the vcf file into plink and the process ended with --vcf 616k variants complete. Error. Out of memory, The --memory flag may be helpful.

and while checking the log folder, I see all 3 bed, bim and fam files created with name-temporary - does this mean the process is incomplete? how to rectify the error. I am using Plink 2.0 version and Ubuntu Linux 20-4

[chrchang523]

Can you post the full .log file from the failed run?

[gimeno]

Hello, here you go. giri@giri-Ubuntu20-4:~$ cd Downloads/Genome/chr22 giri@giri-Ubuntu20-4:~/Downloads/Genome/chr22$ plink --vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf \

--make-bed \ --out converted22 PLINK v1.90b6.18 64-bit (16 Jun 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to converted22.log. Options in effect: --make-bed --out converted22 --vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf

3936 MB RAM detected; reserving 1968 MB for main workspace. --vcf: 616k variants complete. Error: Out of memory. The --memory flag may be helpful.

Answer 3

[gimeno]

hi chrchang523, Just checked the folder, and it seems the completed files can be seen now for the previous runs in the location - I am able to see bed, bim and fam files without -temporary suffix now. Not sure what changed or how they got created. adding a screenshot for ur reference. But as it can be seen, the current run now shows with name-temporary suffix for bed, bim and fam files.

Answer 4

[gimeno]

https://freeimage.host/i/dxI0nR