OliverLin

Yes, in this case, you should make sure bh-sne is installed successfully in 18.04.

Please refer to https://sourceforge.net/projects/sb2nhri/files/MyCC/manual%20of%20MyCC.pdf Two situations: 1) Nothing in 4_CLR_transformation_SNE: You did not set BH-SNE well! To-do: python from tsne import bh_sne If shows “No module” To-do: sudo apt-get install libatlas-base-dev cd tsne-master python setup.py install 2) No 4_ap.png: You have the limited RAM for affinity propagation. Please try:  To increase the memory size if you have.  To increase the minimum contig length (e.g. -t 3000), so...

an output folder is automatically produced in your working directory.

In my test, there was no problem when running MyCC in docker. But please make sure the following pathes in /opt/MyCC.py: fetchMGbin='/opt/fetchMG/bin' apcluster='/opt/ap' prodigal='/opt/prodigal.linux' uclust='/opt/uclustq1.2.22_i86linux64' cdhit='/opt/cd-hit/cd-hit' fetchMG='/opt/fetchMG/fetchMG.pl' Thank you.

It looks like you did not set the path of fetchMG correctely. Would you please check this out?

Was it 11 or 12? It is reasonable when using a different computer.

Thank you for using MyCC's docker and figuring out how to run. For those data we provide in sourceforge, we blasted contigs against their reference genomes to prodcuce the .spe.txt. We did not assign secies to clusters, but assign speces to contigs. Only species names of the exemplars (i.e., cluster's centroid) were shown in the pdf.

Yes, please set a a higher cut-off for contig length. Additionaly, you can lower -lt or -st.