Segmentation fault: 11 with allow(ED)-extra-chr data.

[Stéphanie Arnoux]

%./plink --vcf MisterT.vcf --allow- code ici...extra-chr --recode --out MisterT
...

%./plink --file MisterT --recode12 --out MisterT --allow-extra-chr
...

%./plink --file MisterT --indep-pairwise 50 10 0.1 --allow-extra-chr
Options in effect:
  --allow-extra-chr
  --file MisterT
  --indep-pairwise 50 10 0.1
8192 MB RAM detected; reserving 4096 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (449024 variants, 24 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
449024 variants loaded from .bim file.
24 people (0 males, 0 females, 24 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 24 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.174256.
449024 variants and 24 people pass filters and QC.
Note: No phenotypes present.
Pruned 7 variants from chromosome 27, leaving 0.
...
Pruned 0 variants from chromosome 22668, leaving 1.
Pruned 3 variants from chromosome 22669, leaving 0.
Pruned 0 variants from chromosome 22670, leaving 1.
Pruning complete.  446651 of 449024 variants removed.
Writing...Segmentation fault: 11

%./plink --file MisterT --extract plink.prune.in --make-bed --out TData --allow-extra-chr
Options in effect:
  --allow-extra-chr
  --extract plink.prune.in
  --file MisterT
  --make-bed
  --out TData
8192 MB RAM detected; reserving 4096 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (449024 variants, 24 people).
--file: TData-temporary.bed + TData-temporary.bim + TData-temporary.fam
written.
449024 variants loaded from .bim file.
24 people (0 males, 0 females, 24 ambiguous) loaded from .fam.
Ambiguous sex IDs written to TData.nosex .
Error: No variants remaining after --extract.

Hi everyone,

I find myself having issues with my --allow(ED)-extra-chr data. I am having issues obtaining a .bed file with my version on OSx Yosemite getting the Segmentation fault : 11. I tried on linux and managed to obtain a .bed but with a segmentation fault : 9 when I try to cluster my SNPs.

 

Just to explain I have SNPs from a manual alignment to a medium quality CDS-reference-genome, but I made some filters. And I have 24 accessions that should be clearly clustering seperately (at least my 2 outliers from an other species). So I wish to do a PCA with R or with the admixture software, but there is nothing coming out of my .ped files at the moment. (R packages are also asking for chromosomes assignments).

Thanks a lot if you can try to help me.

[Christopher Chang]

Hi,

Is the OS X run with the 23 Feb development build?  That was the first attempt at getting a mainline build to support a high contig limit; it had an --indep-pairwise bug which was fixed the next day.

If you're having any problems with the 24 Feb builds (it sounds like I broke --cluster?), could you send me the .log file for that?

[Stéphanie Arnoux]

Hi, I just downloaded the 24th Feb version and it solved the --indep-pairwise error.r

But I still cannot get any results out of the mds. and it is a little confusing for me. I mean I obtain written file results but nothing in the mds.cluster2 which uses my names ID in the first and second raw and get a 0 for the entire third raw.

%./plink --file MisterT --cluster --mds-plot 3 --out mds_3 --allow-extra-chr
Logging to mds_3.log.
Options in effect:
  --allow-extra-chr
  --cluster
  --file MisterT
  --mds-plot 3
  --out mds_3

8192 MB RAM detected; reserving 4096 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (449024 variants, 24 people).

--file: mds_3-temporary.bed + mds_3-temporary.bim + mds_3-temporary.fam
written.

449024 variants loaded from .bim file.
24 people (0 males, 0 females, 24 ambiguous) loaded from .fam.

Ambiguous sex IDs written to mds_3.nosex .
Using up to 4 threads (change this with --threads).

Before main variant filters, 24 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.174256.
449024 variants and 24 people pass filters and QC.
Note: No phenotypes present.

Distance matrix calculation complete.
Clustering... done.                        
Cluster solution written to mds_3.cluster1 , mds_3.cluster2 , and
mds_3.cluster3 .
Performing multidimensional scaling analysis (SVD algorithm, 3
dimensions)... done.
MDS solution written to mds_3.mds .
admins-Mac-mini:plink_mac_dev-24Feb starnoux$ more mdr_3.cluster2
mdr_3.cluster2: No such file or directory
admins-Mac-mini:plink_mac_dev-24Feb starnoux$ more mds_3.cluster2
0076 0076       0
0641 0641       0
...
1272 1272       0

Any kind of advise for solving that part? 

Thanks a lot for the efficiency by the way,

S.