biozzq

Hello @oushujun I had the same problem when running the test data. ``` perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate...

Dear @oushujun Yes, I used a new conda environment to install the 2.0; ``` conda create -n EDTA conda activate EDTA conda install -c bioconda edta ``` Best wishes, Zheng...

Dear @oushujun Thanks for your prompt reply. I have removed my old conda env. To keep the dependencies for EDTA, I changed to install the packages using following command, however,...

Dear @lt11 Thank you. I used following command to map the short reads to the graph genome which was constructed by using pggb. The graph genome was constructed using the...

Hi @traxexx Yes, even I use the same reference fasta for generating BAM files, it sometimes give me the errors. Best regards, Zheng zhuqing

Hi I think you can try GenomeSTRiP/Paragraph/graphtyper.

Dear @brentp Thank you. Yes, lumpy_filter is segfaulting when running alone. Since the BAM file was so large, I only attached a small demo generated by `samtools view -s 0.001`;...

Dear @brentp It also gave me seg fault when using these subsets. However, it's very strange when I migrate these files to another compute node, the lumpy_filter runs smoothly. It's...

Dear @brentp The version of lumpy is V.0.2.13 which was installed using anaconda. I think this version should be the most recent. However, I do not know how to set...

Dear @brentp The smoove ran smoothly after installing lumpy by conda in an online environment. The above error occurred when installing lumpy by conda in an offline environment. I found...