FREEC segfaulting at "annotate copy numbers": `cannot create std::vector larger than max_size()`

[dmgie]

Hi,

thank you for the tool. Whilst trying to get FREEC to run for tumor-only somatic WES data, I've been encountering the error

terminate called after throwing an instance of 'std::length_error'
  what():  cannot create std::vector larger than max_size()

which seems to happen after or during the annotate copy numbers step. I have the individual chromosome FASTA files (chrFiles) that I pass to FREEC, the chrLenFile, as well as specifying the target/capture regions from a provided .bed file. I have tried sorting the .bed file to see if that's an issue, but I run into the same problem. The FREEC process usually exits with error code 70 or 96 i.e. <script_path>: 96 Aborted (core dumped) freec -conf config.txt, which then kills the (slurm) job via 134 (SIGABRT). I've tried adjusting the memory and CPU parameters in case that might be causing issues but nothing there either.

Are there things that I could investigate on what might be causing the issue?

Thanks.

[lauratwomey]

I encountered the exact same issue. Other samples from the same run completed successfully, and I cannot figure out the difference with the one particular sample that fails. The config file parameters for WES are the same, the coverage is very similar...
Could you please advice on what to check / what could be causing the issue?
Thank you so much!

cat .command.err
..will use window size equal to the length of each exon
..failed to run segmentation on chrY
terminate called after throwing an instance of 'std::length_error'
  what():  cannot create std::vector larger than max_size()
/scratch/sample1/.command.sh: line 60:    50 Aborted                 (core dumped) freec -conf config.txt

[LangeTo]

Hey,

are there any updates on this issue? I'm experiencing the same issue. I use FREEC inside nf-core's sarek pipeline. Half of my samples run through without an issue and the other half runs into this error:

..calculating medians for 21
..calculating medians for 22
..calculating medians for X
..annotate copy numbers
terminate called after throwing an instance of 'std::length_error'
  what():  cannot create std::vector larger than max_size()
{WORK_DIR}
.command.sh: line 60:    70 Aborted                 freec -conf config.txt

I tried to find differences between working and not working samples by comparing coverage, reads mapped onto X and Y chromosomes, .... but none of the metrics I used showed an obvious difference. Furthermore, I increased resources by 10x, which also did not help. So I'm a bit stuck here, as the .bed file I'm using is the obviously the same for working and non-working samples and the other inputs do not exhibit striking differences...

I'd appreciate any help very much. Thanks in advance 🤞

[valeu]

Dear all, I have never had this error myself. The only way to understand what is going on is to debug the code using your specific sample that causes the error. Would you be interested in sharing the data?