Simon C Chu

Just noticed you have run that step. Not sure why trigger this error `ValueError: invalid coordinates: start (19177217) > stop (19177216)`. Is this WES? Could you test on HG002 (WGS)...

I remember a similar issue was reported on WES before. xTea is mainly developed for WGS, and is not tested that much on WES. I will test more and see...

Hi Phil, Thank you for suggesting this! Agreed! I will provide an option (or skip this one) in the next release. Best, Simon

Yeah, this is in my to-do-list. I'll export a vcf file format. For the current output, each column representation could be find here: https://github.com/parklab/xTea_paper/tree/main/run_tools/xTea/HG002. There is a intermediate file called...

`negative value` indicates the insertion is started/ended from the flanking region (likely to be transduction). But maybe also the reported annotation is incorrect.

It's not straightforward as the reference SVA annotation is fragmented and inaccurate (because of the tandem repeats expansion). For a simple way, just consider position 0 as the start position...

We met the similar issue: *** caught segfault *** address 0x2b1a28320040, cause 'memory not mapped' Traceback: 1: findDistValueByRowColInd(x$distance, attr(x$distance, "Size"), i, higherDensity) 2: findClusters.densityCluster(dataClust, rho = rho_threshold, delta = delta_threshold,...

Hi, does this file exist? `/data/TE_insertion/working/3588/tmp/l_asm_tmp/3500/chr287407875_3500_wtdbg2.ctg.lay.gz`

Will the error repeat if you run `wtpoa-cns -i /data/TE_insertion/working/3588/tmp/l_asm_tmp/3500/chr287407875_3500_wtdbg2.ctg.lay.gz -fo /data/TE_insertion/working/3588/tmp/l_asm_tmp/3500/chr287407875_3500_wtdbg2.ctg.lay.fa -t 16` ?

I think it's an error happed earlier before this step that generated empty files. But not sure exactly at which step. Could you try to run with a larger memory?