"Pathologically long" line error with legitimate structural variants

[user98]

Hi, 

I'm working with a callset that contains SVs, very few of which are very long. I keep hitting the error "Pathologically long" line, even though these are legitimate variants. 

Here is a log:

PLINK v1.90b3.44 64-bit (17 Nov 2016)      https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to callset_EUR_with_cms_chr2.oxford.inf.10kb.cM.log.
Options in effect:
  --cm-map genetic_map_hg38_withX_chr2.txt 2
  --keep-allele-order
  --make-bed
  --map callset_EUR_with_cms_chr.2.inf.10kb.bim
  --out callset_EUR_with_cms_chr2.oxford.inf.10kb.cM
  --ped callset_EUR_with_cms_chr.2.ped
  --zero-cms

257564 MB RAM detected; reserving 128782 MB for main workspace.
Error: Line 907969 of .map file is pathologically long.

Is there any way at all to tell plink to just ignore this and continue? 

Thanks, 

[Christopher Chang]

No, plink does not support variant IDs of length >16000; if you have a .map file with longer IDs, you are responsible for shortening them before providing them to plink.

[Christopher Chang]

(To be clear, the structural variants may be legitimate, but the variant IDs that have been assigned to them are not legitimate and must be fixed.)

[user98]

The variant IDs have already been shortened, it seems it's the alleles themselves in the .bim that plink is complaining about (I checked line 907969 manually). Strangely, I haven't run into this issue when generating the bed/bim/fam from a vcf or adding cM to the bims from a genetic map. 

[Christopher Chang]

Well, the .log you posted referred to a .map file so I tried to help with that.  If your real problem is with a .bim, I need to see a .log file which exhibits it.

plink 1.9 and 2.0 are supposed to be able to handle allele codes of length up to a few tens of millions.

[Christopher Chang]

...oh, I now see that you provided a .bim file to --map.

Try generating an actual .map file that contains only the first four columns of that .bim.  "cat [input .bim file] | cut -f 1-4 > [new .map filename]"

[Javier Maravall]

That worked, thanks a lot!

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