pureclip coredumps

[riederd]

Hi,

the following pureclip command crashes with a coredump:

pureclip -i umidedup.bam -bai umidedup.bam.bai -g homo_sapiens.88.fa -iv '1;2;3;4;8;16' -nt 8 -o PureCLIP.crosslink_sites.cov_CLmotifs.bed -nim 4 -fis fimo_clmotif_occurenc
es.bed

Last few output lines of stderr:

terminate called recursively
terminate called after throwing an instance of 'terminate called recursively
boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::domain_error >'
command.sh: line 5: 63589 Aborted (core dumped) pureclip -i umidedup.bam -bai umidedup.bam.bai -g homo_sapiens.88.fa -iv '1;2;3;4;8;16' -nt 8 -o PureCLIP.crosslink_sites.cov_CLmotifs.bed -nim 4 -fis fimo_clmotif_occurences.bed

[skrakau]

Hi,

I assume you are using PureCLIP v1.3.1 ?
Could you send me the log file when running it with -vv then I can have look? In case you have data you could share where I could reproduce the error this would also help.

Best,
Sabrina

[riederd]

Hi,

you are right it is v1.3.1.
I attached the log obtained with -vv, if this is not enough, I can send you the data, let me know.

PureClip.log

[skrakau]

Hi,

sorry for the late reply. It seems that there are relatively few signals in the regions used for parameter learning, in your case chr. 1 - 3. PureCLIP discards regions with only one read starting within 4 bandwidths. After this only 15 regions remain, which might cause a problem during model training. You could try to omit the '-iv' parameter in order to use all given data for parameter learning, maybe that helps.

However, in general this problem should of course be handled differently. If you could send me the data to reproduce the error in a private message I will try to address this in the future.

Best,
Sabrina

[riederd]

Hi, I just wanted to ask if you did get my private message via filesender with the data?
I sent it on Dec. 10 to your (?) University address.

[skrakau]

Hi,

yes thanks, I got the link and downloaded the data, but didn't deal with the problem yet.

[eric-yyjau]

Hi @skrakau ,

I installed the package from conda.
When I run the program, the process killed itself.

pureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai \
 -g ref.hg19.fa -iv 'chr1;chr2;chr3;' -nt 0 \
 -o PureCLIP.crosslink_sites.bed \
 -ts 6000 -mtc2 5000 -nta 0 -vv >> log_0817_v2

• snippets before process got killed
  log_0817_v2.txt

Simple linear regression (count <- kde): b0 = -0.168431 and b1 = 111.308 .
  Compute KDEs ...
  Estiamte Ns ... 1
Prior ML estimation of density distribution parameters using predefined cutoff ...
Initial gamma1: Run simplex algorithm using different start points.
updateThetaAndK... kMax: 1
Call GSL multimin solver nmsimplex2 ...

• pureclip version

pureclip - Protein-RNA interaction site detection 
==================================================
    pureclip [OPTIONS] <-i BAM FILE> <-bai BAI FILE> <-g GENOME FILE> <-o OUTPUT BED FILE>
    Try 'pureclip --help' for more information.

VERSION
    Last update: April 2019
    pureclip version: 1.3.1
    SeqAn version: 2.2.0

This (https://hub.docker.com/layers/ubuntu/library/ubuntu/xenial-20200706/images/sha256-e5ec578bd8c334d7c9849fd9bbaa78ec25f2b51b0bf7c9e18b1e9b7ca32d6681?context=explore) docker image.

Thanks.