Closed LouisLeNezet closed 1 year ago
I thought I found the problem. The files had a really long name and by shortening it the error disappeared. But I still encounter this problem from time to time...
The error look as follow
[SHAPEIT5] Ligate (ligate multiple output files into chromosome-wide files)
* Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne
* Contact : simone.rubinacci@unil.ch & olivier.delaneau@gmail.com
* Version : 5.0.1 / commit = 1.0.0 / release = 2023-02-10
* Run date : 17/02/2023 - 19:34:35
Files:
* Input LIST : [all_files.txt]
* Output VCF : [1.vcf.gz]
* Index output : [NO]
Parameters:
* Seed : [15052011]
* #Threads : [2]
Read filenames in [all_files.txt]
* #files = 2
Ligating chunks
* Creating file descriptor
* #samples = 1
Cnk 0 [chr21:0-1] [L=0]
Buf 0 [chr21:16650034-16749830] [L_isec=1397 / L_tot=2042] [Avg #hets=5] [Switch rate=1] [Avg phaseQ=28.2288]
.command.sh: line 8: 52633 Segmentation fault SHAPEIT5_ligate --input all_files.txt --thread 2 --output 1.vcf.gz
Hi,
The log file looks very suspicious. The first chuck has zero(?) variants and all the rest is detected in the buffer. The intersection has only 5 hets, that's odd too. I am very curious to see your files/chunks. Is that possible?
Thank you for reporting this and for your work with SHAPEIT/GLIMPSE!
Hi,
You can find the files in my github repository on the branch imputation.
The data used are in data/test
for the one who works and data/test_error
for the one who doesn't work.
The command I used in each folder is the following:
SHAPEIT5_ligate --input all_files.txt --output test.vcf.gz
And I used the SHAPEIT5 build with bioconda.
Maybe the problem come from there ? I have to admit that I didn't look into detail when writing the recipe.
I just copy pasted what I've done on GLIMPSE2 and as it worked nearly first try I didn't checked more.
I just checked this morning and this some trouble with the repo.
Hi @srubinacci, I think I found the problem... The thing is that the file in the input file need to be ordered, right ? And in my pipeline it wasn't always the case (explaining the randomness of the error). I also found that the path can't have a space, it will also generate the same error if so.
Hi, I see. Indeed, the data need to be ordered and indexed. Indexing gives a way to access to the file in random access, but also requires the VCF/BCF file to be ordered.
Hi ! I'm developing Shapeit5 on nf-core now and I currently on a
Segmentation fault
when usingSHAPEIT5_ligate
. The problem is that this error arise randomly and I don't quite understand why for the moment. You can find all the code here. But the command is simply as follow:Where all_files.txt as just two files generated by
SHAPEIT5_phase_common
.Do you have an idea which kind of error is behind ?