Annotation with MitFi fails (v1.4)

[MareikeJaniak]

Hi Rémi, hi Frederic,

I thought it would be better to put this in a new issue. I downloaded version 1.4 and ran MitoFinder on the test_case files.

It looks like the annotation step fails, but I'm not sure why. I'm attaching the stdout file and the geneChecker.log.

The file geneChecker_error.log has the following message:

ln: failed to create symbolic link './cmsearch': File exists Traceback (most recent call last): File "/home/mcj43/software/MitoFinder/geneChecker_fasta.py", line 452, in tRNAs = assemblyCheck.tRNAs AttributeError: 'bool' object has no attribute 'tRNAs'

Let me know if you need anything else!

Best, Mareike

geneChecker.log.txt test_MitoFinder.out.txt

[RemiAllio]

Hi Mareike,

Thank you for your feedback. In fact, it seems that the tRNA annotation step failed.

Could you please check if the file [SeqID]_mitfi/*.mitfi exists and if mitfi found some hits ? If not, do you have java installed in the computer running MitoFinder ?

Thank you, Best, Rémi

[MareikeJaniak]

Hi Rémi,

I don't see a directory that is [SeqID]_mitfi.

The following file exists but it is empty: [SeqID]/[SeqID]_MitoFinder_megahit_mitfi_Final_Results/[SeqID]_mtDNA_contig.mitfi

Yes, I do have java installed.

Let me know if I should try anything else!

Best, Mareike

[RemiAllio]

Hi Mareike,

Well, I don't know what happened, sorry about that!

Just to be sure I have all the elements to think about it, could you please:

• confirm that you downloaded MitoFinder with git clone ?
• confirm that you run the install.sh ?
• tell me if something is written in the geneChecker_error.txt file
• and eventually, run java -jar path/to/MitoFinder/mitfi/mitfi.jar [SeqID]_link.scafSeq

Thank you so much and sorry for the inconvenience... Best, Rémi

[MareikeJaniak]

Hi Rémi,

Sorry for the delay, I just saw your response.

Yes, I downloaded MitoFinder with git clone and ran install.sh.

The geneChecker_error.log file contains the following:

ln: failed to create symbolic link './cmsearch': File exists Traceback (most recent call last): File "/home/mcj43/software/MitoFinder/geneChecker_fasta.py", line 452, in tRNAs = assemblyCheck.tRNAs AttributeError: 'bool' object has no attribute 'tRNAs'

When I run the java -jar line, I get the following error:

MiTFi - mitochondrial tRNA finder v0.1 Exception in thread "main" java.io.IOException: Cannot run program "./infernal-1.0.2/src/cmsearch": error=2, No such file or directory at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1128) at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1071) at java.base/java.lang.Runtime.exec(Runtime.java:589) at java.base/java.lang.Runtime.exec(Runtime.java:413) at java.base/java.lang.Runtime.exec(Runtime.java:310) at mitfi.Main.main(Main.java:228) Caused by: java.io.IOException: error=2, No such file or directory at java.base/java.lang.ProcessImpl.forkAndExec(Native Method) at java.base/java.lang.ProcessImpl.(ProcessImpl.java:319) at java.base/java.lang.ProcessImpl.start(ProcessImpl.java:250) at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1107) ... 5 more

Maybe this has something to do with the first line of the geneChecker_error.log? I hope this helps!

Best, Mareike

[MareikeJaniak]

Hello again!

The problem seems to be solved! It was indeed an issue with java. I was sending the MitoFinder command out as jobs on our cluster and I didn't load the java module within the job scripts, because it's usually not necessary.

I just tried it again with the java module loaded within the job script and it ran without issues!

Sorry for not realizing that sooner. My fault!

Best, Mareike

[RemiAllio]

Hi Mareike!

Thank you for the update. I will see how I can improve the error/log files to help the users to find what happened! Let us know if MiTFi find similar or better results than tRNAscan-SE 2!

Best, Rémi