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zhenchengfang / PlasGUN

Gene prediction in plasmid metagenomic short reads using deep learning.
GNU General Public License v3.0
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[Matlab error] FileAccessError exception #1

Open Arzhura opened 4 years ago

Arzhura commented 4 years ago

Hello, Thank you for developing this tool, I would love to use it but I get this error concerning Matlab even if I have the right version loaded. Capture d’écran 2020-07-22 à 11 03 01

Can you help me ? Thank you in advance

zhenchengfang commented 4 years ago

Thank you for your interest in PlasGUN. We have realized that installing the dependent software may be difficult in different machine environment. Therefore, we have released a virtual machine in which all dependent software has been installed. The virtual machine can be downloaded at http://cqb.pku.edu.cn/ZhuLab/PPR_Meta/VM_Bioinfo.vdi.7z. The package of PlasGUN is on the desktop of the virtual machine. Also, you can refer to the manual (http://cqb.pku.edu.cn/ZhuLab/PPR_Meta/Manual-v1.1.pdf) to see how to install the virtual machine (quite easy). Note that the manual is for PPR-Meta, a tool that we released eariler, but the approaches of installing the virtual machine for both PPR-Meta and PlasGUN are the same! We will also updated the manual of PlasGUN as soon as possible. Any question, please do not hesitate to contact me.

Arzhura commented 4 years ago

Hello, Thank you, I have seen for the virtual machine, but I currently work on a cluster, this way I can not transfer the virtual machine on the cluster (no interface), or I don't know how to do it. Perhaps you can help me on this. Otherwise my computer is not enough powerful to handle good calculation condition through a virtual machine installation. Thank you in advance.

zhenchengfang commented 4 years ago

Emm...We tried to ascertain the cause of the problem, but it seemed that this problem might be caused by the machine environment and did not occur in our machine. We are very sorry that we are hard to solve this problem remotely. Maybe you can try to run PlasGUN using the MATLAB script rather than the executable file. In this way, you only need to install the MATLAB rather than the MATLAB Component Runtime (MCR). We will try to build a bioconda recipe for PlasGUN in the future. We apologize for this problem again.

Arzhura commented 4 years ago

Hello, I just test the Virtual box I already install previously (I was using PPR-meta too) I don't know if it is a mistake that make sense to you but I got this error: Capture d’écran 2020-07-30 à 18 02 38 I launch the test also and it has work, so why the Fasta file I am using is aborted ? View of the test: Capture d’écran 2020-07-31 à 12 23 06

I try to solve also the problem on the cluster but I end up with conflict between numpy version 1.13.1 and Keras 2.0.8 and numpy is not detected: Capture d’écran 2020-07-31 à 14 42 02 I try to solve this conflict hardly but I don't find a solution at this point. I don't know how you can have such version for requirements, they are all create conflict.

So I made another Conda env installation without taking care of the version and now I got this error: Capture d’écran 2020-07-31 à 15 24 36 I don't know how to launch the Matlab script directly from the command line it is not describe in the manual. I try with the example.fna:

Capture d’écran 2020-07-31 à 15 48 01 I try many solution I am quite desesparate I must to admit now... I don't know if you can really help me but I would love too Thank you in advance

zhenchengfang commented 4 years ago

Would you please send me your FASTA file through the e-mail? It seems that the problem is caused by the tool MetaTISA, a software released earlier which is called by PlasGUN.

Arzhura commented 4 years ago

Yes I will thank you !

Arzhura commented 4 years ago

Hello, I send you an email to this address is that the correct one ? fangzc@pku.edu.cn Thank you in advance & have a nice day

zhenchengfang commented 4 years ago

I just replied to your email. Please check it!