BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

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Segmentation fault #79

Open jfnavarro opened 3 years ago

jfnavarro commented 3 years ago

I am trying to run Control-FREEC on a set of samples (WES) and I get segmentation faults in some of the samples while others complete fine.

..Annotation of CNVs for X
1   0.00875069
2   0.935849
3   0.0070744
4   0.0478207
5   0.000315901
6   3.9343e-05
15  2.07169e-06
zsh: segmentation fault  freec -conf config.txt

Is this something expected? Thanks!

valeu commented 3 years ago

Dear user, no, it is not expected.. But still happens sometime. To help you I will need your config file and the complete output into the command line. Thank you Valentina

jfnavarro commented 3 years ago

Dear Valentina,

I've attached here both the config and the console output files.

Best, Jose out.txt config.txt

jfnavarro commented 3 years ago

Hi, have you been able to look at this issue?

valeu commented 3 years ago

Dear José Fernández,

From your output, it is difficult to say what exactly caused the error. Can you tell me which files have been created?

Also, can you try to run this simplified config, please, and let me know whether it created an error?

[general] BedGraphOutput = TRUE chrFiles = /Users/jfnavarro/Projects/Scitron/Results/Chromosomes chrLenFile = /Users/jfnavarro/Projects/Scitron/Results/Homo_sapiens_assembly38.len

forceGCcontentNormalization = 1

maxThreads = 8

minimalSubclonePresence = 30

ploidy = 2,3

ploidy=2 sex = XX readCountThreshold = 50 breakPointThreshold = 1.2 breakPointType = 4 window = 0

[control] inputFormat = pileup mateFile = B190986_RG1297_32_gDNA.pileup mateOrientation = FR

[sample] inputFormat = pileup mateFile = 1297_34_cfDNA.pileup mateOrientation = FR

[BAF] SNPfile = /Users/jfnavarro/Projects/Scitron/Results/dbsnp_138.hg38.vcf.gz

[target] captureRegions = /Users/jfnavarro/Projects/Scitron/intervals/intersect_collapsed.bed

jfnavarro commented 3 years ago

Dear Valentina,

Thanks for your reply. So, I played a bit and I got to learn that it was the minimalSubclonePresence = 30 parameter the one causing troubles even though 30 is the recommended value for WES data. I think for now I will not use that option since it is not really needed for the post-analysis.

Best, Jose

valeu commented 3 years ago

Good to know. The subclonal search is still in Beta. Hope to debug it when have time.

Sent from my iPhone

On 10 Dec 2020, at 14:55, José Fernández Navarro notifications@github.com wrote:

Dear Valentina,

Thanks for your reply. So, I played a bit and I got to learn that it was the minimalSubclonePresence = 30 parameter the one causing troubles even though 30 is the recommended value for WES data. I think for now I will not use that option since it is not really needed for the post-analysis.

Best, Jose

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