MyCC not producing any bins

Question

[h.l.wong]

Hi all,

I have been using MyCC to generate draft genomes but it no bins were produced. The folders 1_Data to 7_AllClusters were here though.

My command line is :

MyCC.py contig.fa -a depth.txt -t 2000 -keep

I checked the log and everything is alright. Is there anything wrong with my script?

Cheers

Alan

[Kevin Blighe]

Hi Alan, have you installed all of the Python dependencies? They appear to be listed here: https://sourceforge.net/projects/sb2nhri/files/MyCC/

Also, is your contig length specified by -t 2000 too long? If you try the default of 1000, does it change anything?

[suran.nambisan]

Hi All

I have used MyCC.py but am not able to get any output except the log file.

MyCC.py mg_scaffolds.fa

Could you please help?

Thanks

Suran

[Kevin Blighe]

...and what does that log file state? Look for warning and/or error messages.

[suran.nambisan]

20190217_1355
1_rename.py /home/group_ss1/Suran/Data_MyCC/Ahk_umapped_scaffold.fa 1000
Seqs >= 1000 : 84268
Minimum contig lengh for first stage clustering: 1269
run Prodigal.
/home/group_ss1/software/MyCC_related/Tools/prodigal.linux -i My.fa -a gene.aa -d gene.nuc -f gbk -o output -s potential_genes.txt
run fetchMG.
run UCLUST.
Get Feature.
2_GetFeatures_4mer.py for fisrt stage clustering
2_GetFeatures_4mer.py for second stage clustering
3_GetMatrix.py 1269 for fisrt stage clustering
 59002 contigs entering first stage clustering
Clustering...
1_bhsne.py 20
2_ap.py /home/group_ss1/software/MyCC_related/Tools/ap 500 0
Cluster Correction.
to Split and Merge.
1_ClusterCorrection_Split.py 40 2
2_ClusterCorrection_Merge.py 40
Get contig by cluster.
20190217_1421

[suran.nambisan]

Hi Kevin.

Sorry for late reply and sorry for the mess above. Is there a way to attach the log file?

I did not see any errors. And the tool just ran and ended. I saw it did produce intermediate files but since -keep was not used they were removed and finally only this log remains. I followed the website posted above for installation. The OS of the system was Ubuntu 18.04. During installation "libatlas-dev libatlas3gf-base" were not installed but rest of the things were installed or were presen in the system.

Could you please suggest what could be wrong?

Thanks and regards

Suran

[Kevin Blighe]

Hey Suran. No problem. For your first post, I have edited it and wrapped your text using the 101 010 button, which improves formatting of code. I have also moved both of your recent posts to comments (you had posted the as answers - I am aware that the system is confusing, though).

MyCC is obviously not the most commonly-used program, as you can probably appreciate. Perhaps you could run it again with -keep so that you can check the output at each step. Also, which Python version do you have - just type python --version

It could also be that the program does not function as expected on Ubuntu 18.04. It seems to have been developed on 14.04. I would aim to solve the dependency issues, e.g., libatlas-dev libatlas3gf-base, as these may also be the problem.

[suran.nambisan]

Hi Kevin

Thanks for your reply. The python version is given below: Python 2.7.13 :: Continuum Analytics, Inc.

Let me follow up on your suggestions and then I will get back to you. regards Suran

[Kevin Blighe]

Thanks, but remember to use the ADD REPLY or ADD COMMENT button the next time when you post a message. I have moved this to a comment, too.

[suran.nambisan]

Hello Kevin

MyCC.py worked on Ubuntu 16.04 OS and produced output files after clustering.

Thanks Suran

[Kevin Blighe]

Okay, then you know that it is an issue with Ubuntu 18.04. You may consider posting on the Ubuntu forum and discuss those libraries that could not be installed. It could be that they are called something different between 16.04 and 18.04, which has happened before.

Perhaps you could manually try to install this: https://packages.ubuntu.com/bionic/libatlas-base-dev