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xunchen85 / ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.

Home Page:http://www.uvm.edu/genomics/software/ERVcaller.html

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Cannot remove "sort.bam.tmp.0000.bam" files

xxYaaoo opened this issue · comments

commented

Hello, Dr. Chen,

Recently, I met a problem that after completing the whole pipeline, sometimes there were still lots of "sort.bam.tmp.0000.bam" files left in the output folder, while sometimes they were removed, but I set the same CPU and Mem parameters for each running. I am not sure whether the output vcf file is complete if the bam files are not removed. What might cause this problem and how could I fix it？

Thank you！

commented

Hi,

this error was induced by the samtools sort step which may be because of "out of memory" or "running time". it usually indicates the job was not finished yet. you will see an empty vcf file unless you already re-run it with the same sample names.

thanks,
xun

commented

ok, thank you for your answer! I will continue to adjust my parameters.~