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DerKevinRiehl / transposon_annotation_reasonaTE

Transposon annotation tool "resonaTE" (part of TransposonUltimate)
GNU General Public License v3.0
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error in MUST component #4

Closed bishopia closed 2 years ago

bishopia commented 2 years ago

I'm working through your reasonaTE pipeline now and am having trouble with MUST annotation. Have you seen the following error or know how to correct/fix it? I snagged just the first few lines from stdout, but it goes on forever.... Best, Ian

(transposon_annotation_tools_env)[ibishop@node1163 res1]$ reasonaTE -mode annotate -projectFolder workspace -projectName ref_euk -tool must
Spliting the genome into 10 sub-genomes ...  [SubFiles:10] [done] [Elapsed time: 0 seconds]
Scanning the nucleotide sequences for potential MITEs ... Total calculation time elapsed: 561 seconds.
Loading the annotation data ...  [RawMITEs:295] [done] [Time:0 seconds]
Removing redundancy in the predicted MITEs ... Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
Use of uninitialized value $newB in array element at /gpfs/home/ibishop/data/ibishop/condas/transposon_annotation_tools_env/bin/MUST.r2-4-002.Release/MUST_Pipe.pl line 119.
gqpx commented 2 years ago

I am having the same issue...

DerKevinRiehl commented 2 years ago

Dear bishopia and gqpx, thanks for raising this issue!

Unfortunately, I am not the author of MUST, and just converted MUST into a conda package to integrate it into my tool.

The code can be found here: https://github.com/DerKevinRiehl/transposon_annotation_tools/blob/main/transposon_annotation_tools_mustv2/MUST.r2-4-002.Release/MUST_Pipe.pl

The "uninitialized value $newB" actually is mentioned in Line 117 and 119. I am not sure why this error happens.

Could you please give me...

Moreover, can you try to run the original MUSTv2 on your machine? http://www.healthinformaticslab.org/supp/resources.php It would be interesting to see if you have the same issue with the original code (I didnt change it a lot).

Thank you very much for your answers in advance, Best regards, Kevin

gqpx commented 2 years ago

I am using genome GCF003344945.1 as a test. The genomes for the analysis itself will not be annotated. Please find the summary of our CONDA environment below. I also tried to use a native version of MUST, but the -tool_ flag only accepts the implemented options.

envname.txt

bishopia commented 2 years ago

The error disappeared when i ran your must tool on GCA_000149405.2. As for the draft assembly I had an issue with, could i send it privately?

DerKevinRiehl commented 2 years ago

Dear gqpx and bishopia, sorry for the late reply and thank you very much for your answers and useful sugestions. I should be available more from now on with answering Github issues.

@gqpx

Dear GPQX thanks for sharing your environment. I tried to find differences between your ENV and my setup, using https://text-compare.com/de/. What I found is attached to this post in the Comparison.pdf. What we can find from this comparison (left column is yours, right column is mine) is actually a lot ^^, probably because we have different base environment setups. As MUSTv2 is a perl based tool, I checked the perl conda packages. Except for some very small packages, I dont see lots of differences between our environments. I would like you to try to delete the environment and just reinstall it. Could you please try to run it with the demo fasta file that I provide in the tutorial and tell me, if you got the same error again?

@bishopia

I think that is very strange that it works for some genomes, and for others not. Are you sure you are getting the same error? Did you retry multiple times? From my point of view this error is related to a wrong setup of the conda environment, as its about a syntax problem of the must code itself rather than anything possibly related to the genome.

Best regards, Kevin Riehl