Simon C Chu

Sorry for the late reply. Could you post the error message?

Change this: ``` SAMTOOLS_PATH GLOBAL /usr/bin/samtools JELLYFISH_PATH GLOBAL /usr/bin/jellyfish VELVET_PATH GLOBAL /usr/bin/ ``` to: ``` SAMTOOLS_PATH /usr/bin/samtools JELLYFISH_PATH /usr/bin/jellyfish VELVET_PATH /usr/bin/ ``` Also, please check whether your python is properly...

Hi @Milad021 , Yes, it is important. Have you tried to re-compile TERefiner_1? Also, check the input of TERefiner, whether they are empty or not.

I think you need to set the bamtools path in the makefile (under TERefiner folder). Usually, it works well and don't need to re-compile. But I do need to release...

Can you post the reported errors by running this command? ``` /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa -o ./Siek14_Repeatelm_12X/contigs.fa _no_dup.fa -c 0.9 -g ```

In case you will meet other issues, you can similarly compile ContigsMerger on your server. Then copy the newly compiled TERefiner_1 and ContigsMerger to the same level as main.py. Then...

I think the error is caused before this step. The /Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam is empty? Also, can u similarly compile ContigsMerger on your server. Then copy the newly compiled TERefiner_1 and ContigsMerger...

Can u view this file? ``` samtools view contigs.fa.itself.sort.bam NODE_1_length_176_cov_1.988636_30_31235_312356 ```

I mean this file: ./Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam, because u said: ``` By running this command, I have this error message : """""""""""" $ /usr/local/src/REPdenovo/TERefiner_1 /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa...

Thank you for the suggestion! We are planning to release a docker version. We will release a python 3 version at the same time.