When run Mitofinder met a problem

[kuangzhuoran]

Traceback (most recent call last): File "/data/01/user164/workspace/try/MitoFinder/mitofinder", line 1205, in rename = Popen(args1, stdout=open(os.devnull, 'wb')) File "/usr/lib64/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

upon is the error,and i also attach the log file Mf_MitoFinder.log

I dont know what should i do Thank u so much

[RemiAllio]

Hi,

Thank you for your message.

Please, could you give me more information about the system in which you are running MitoFinder (Linux/MAC/Windows)? Also, what is your default python environment? python2.7 ?

Cheers, Rémi

[kuangzhuoran]

Hi ! Thanks for replying. I run mitofinder on Linux(Xshell), default python is python3.7, but I have also installed py2.7

First error I met is "bad interpreter: user/bin/python: no such file or directory"; so I "vim mitofinder/rename_fasta_seqID.py", and I change the first line"usr/bin/python"(python3.7) to "usr/bin/python2"(python2.7)

I have resolved the above problem, maybe. the error is on line 1205, I add "shell = True" in parentheses，like " Popen(args1, shell=True, stdout=open(os.devnull, 'wb'))". And I rerun mitofinder, the error is the same, but on different line, Repeat this until no error is reported .

Now I meet a new error, like

Traceback (most recent call last): File "/data/01/user164/workspace/try/MitoFinder/mitofinder", line 1337, in
if check_if_string_in_file(pathtowork + "/geneChecker.log","MiTFi failed.") or (os.stat(pathOfFinalResults+"MiTFi.log").st_size != 0 and not check_if_string_in_file(pathOfFinalResults+"MiTFi.log","hits")) :

OSError: [Errno 2] No such file or directory: '/data/01/user164/workspace/mito_test/mito_test_MitoFinder_mitfi_Final_Results/MiTFi.log'

MitoFinder.log

[RemiAllio]

Hi,

I am really sorry for the delay...

Since the installation seems to be complexe in your environment, I would like to try something else. I am trying to develop a MitoFinder image using Singularity.

I have built an image for you and you should be able to download it here: MitoFinder_1.4.sif

This is a temporary link, but if it works for you, I will make it permanent for everyone.

The only thing you need to do is to install singularity (it should work using sudo apt install singularity. If not, you should find out how to install it here). Then, you should be able to run mitofinder as follows:

PATH/TO/MitoFinder_1.4.sif -j [seqid] -1 [left_reads.fastq.gz] -2 [right_reads.fastq.gz] -r [genbank_reference.gb] -o [genetic_code] -p [threads] -m [memory]

Please, tell me if it works and if you found it easy to run. Best regards, Rémi

[kuangzhuoran]

Hi ! Thank you for your help! I am so sry I dont reply in time

I have tried this now, I use "conda install singularity" to install singularity,because I dont have root / permission. And I met a ERROR, I have tried this in python3.8 and python3.7

ERROR : Unknown image format/type: ./MitoFinder_1.4.sif ABORT : Retval = 255

I am trying to solve this erroe.

[RemiAllio]

Hi,

So, just to be sure: when you run singularity --version the command works and give you the version of singularity installed? Then, when you try ./MitoFinder_1.4.sif from the directory containing the program, you have the error, right?

[kuangzhuoran]

Hi ! yes~ singularity -v Increasing verbosity level (2) Singularity version: 2.4.2-dist

[RemiAllio]

Hi!

All right, it seems that you have installed a really old version of singularity. The issue may come from that. Could you install a more recent version? I'm afraid you'll probably have to ask someone who has permission to install it (install singularity).

Tell me if it is possible and if it works. Sorry for the inconvenience.

Best regards, Rémi

[kuangzhuoran]

Hi ! so sorry I have asked the administrator to help me install this software， but he told me that He tried for a long time and couldn't install it。 I will try on another server。

[kuangzhuoran]

Hi !
After I changed the server and installed singularity correctly, it can work normally. Thanks for your help!!!!!

Best Regards, kzr

[RemiAllio]

Hi!

Thank you for the good news! I am very happy that it works for you.

The singularity container is now available here!

Best regards, Rémi