Dependency error even when creating conda env with EDTA.yml

[smorzechowski]

I see many people have had the same error message I received:

Error: The RMblast engine is not installed in RepeatMasker!

This is despite installing in the recommended way that freezes all the dependency versions -- conda env create -f EDTA.yml

Why would this dependency error still be occurring?

[smorzechowski]

For those who may be interested, it may be due to the fact that I have a version of perl locally installed. I was getting the following error when I tried to access the version of RepeatMasker installed in the conda environment:

(EDTA) [smorzechowski@holy7c16606 ~]$ RepeatMasker --help
/n/home09/smorzechowski/.conda/envs/EDTA/bin/perl: symbol lookup error: /n/home09/smorzechowski/perl5/lib/perl5/x86_64-linux-thread-multi/auto/List/Util/Util.so: undefined symbol: Perl_xs_apiversion_bootcheck

But, I found this blog, which had the same issue -- https://www.jianshu.com/p/a90a8a47cc8f

Including the following in my sbatch script appears to have fixed the issue --

export PERL5LIB=/

[oushujun]

Thank you for finding out the issue! I think this will help many others. - Shujun

[Zhenlisme]

I got this warning information: "WARNING- Grid computing is not available because DRMAA not configured properly: Could not find drmaa library. Please specify its full path using the environment variable DRMAA_LIBRARY_PATH". Will this influence the result?

[HejunLu]

I see many people have had the same error message I received:

Error: The RMblast engine is not installed in RepeatMasker!

This is despite installing in the recommended way that freezes all the dependency versions -- conda env create -f EDTA.yml

Why would this dependency error still be occurring?

I meet the same problem with you, when I run several genomes in a bash cycle, the first genome finish with out erro,while from the second genomes, the erro comes: below is the last 100 lines of my logfile, here the first four lines are the perfect finish end information of the first genome, while the cycle run begin failed from the second genome to the end... below is the last 100 lines of my logfile:

Thu Jun 16 06:27:44 CST 2022 Evaluation of TE annotation finished! Check out these files:

                            Overall: SM3H.fa.mod.EDTA.TE.fa.stat.all.sum
                            Nested: SM3H.fa.mod.EDTA.TE.fa.stat.nested.sum
                            Non-nested: SM3H.fa.mod.EDTA.TE.fa.stat.redun.sum

########################################################

Extensive de-novo TE Annotator (EDTA) v1.9.6

Shujun Ou ([email protected])

########################################################

Thu Jun 16 06:27:47 CST 2022 Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

########################################################

Extensive de-novo TE Annotator (EDTA) v1.9.6

Shujun Ou ([email protected])

########################################################

Thu Jun 16 06:28:09 CST 2022 Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

########################################################

Extensive de-novo TE Annotator (EDTA) v1.9.6

Shujun Ou ([email protected])

########################################################

Thu Jun 16 06:28:17 CST 2022 Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

########################################################

Extensive de-novo TE Annotator (EDTA) v1.9.6

Shujun Ou ([email protected])

########################################################

Thu Jun 16 06:28:28 CST 2022 Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

[oushujun]

Hello @HejunLu,

Did you have the same error on other genomes or if you rerun EDTA on this genome, did you receive the same error?

On a side note, you may want to update EDTA to 2.0.

Best, Shujun

[MCampos92]

I'm having some problems with EDTA, when I run it with test data it gives me an error with Hmmer, that it's installed with mamba install edta, and also I tried to install separately. I remove the environment (EDTA) and tried to install everything again but the error persist.

Thanks in advance.

########################################################

Extensive de-novo TE Annotator (EDTA) v2.0.1

Shujun Ou ([email protected])

########################################################

Tue Sep 20 00:57:58 PDT 2022 Dependency checking: All passed!

    A custom library ../database/rice6.9.5.liban is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.

    A CDS file genome.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.

    A BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.

Tue Sep 20 00:58:01 PDT 2022 Obtain raw TE libraries using various structure-based programs: Tue Sep 20 00:58:01 PDT 2022 EDTA_raw: Check dependencies, prepare working directories.

Tue Sep 20 00:58:03 PDT 2022 Start to find LTR candidates.

Tue Sep 20 00:58:03 PDT 2022 Identify LTR retrotransposon candidates from scratch.

Error: hmmsearch is not found in the HMMER path ! awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading (No such file or directory) Warning: LOC list - is empty.

    perl rename_LTR_skim.pl target_sequence.fa LTR_retriever.defalse

Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3

Tue Sep 20 00:58:13 PDT 2022 Warning: The LTR result file has 0 bp!

Tue Sep 20 00:58:13 PDT 2022 Start to find TIR candidates.

Tue Sep 20 00:58:13 PDT 2022 Identify TIR candidates from scratch.

Species: others

[oushujun]

You may want to check which hmmer is in ENV by using ´which hmmsearch´. Sometimes you need to clear your ENV for example with module purge.

Shujun

On Tue, Sep 20, 2022 at 4:02 AM Miguel Campos @.***> wrote:

I'm having some problems with EDTA, when I run it with test data it gives me an error with Hmmer, that it's installed with mamba install edta, and also I tried to install separately. I remove the environment (EDTA) and tried to install everything again but the error persist.

Thanks in advance.

######################################################## Extensive de-novo TE Annotator (EDTA) v2.0.1 Shujun Ou ( @.***)

########################################################

Tue Sep 20 00:57:58 PDT 2022 Dependency checking: All passed!

A custom library ../database/rice6.9.5.liban is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.

A CDS file genome.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.

A BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.

Tue Sep 20 00:58:01 PDT 2022 Obtain raw TE libraries using various structure-based programs: Tue Sep 20 00:58:01 PDT 2022 EDTA_raw: Check dependencies, prepare working directories.

Tue Sep 20 00:58:03 PDT 2022 Start to find LTR candidates.

Tue Sep 20 00:58:03 PDT 2022 Identify LTR retrotransposon candidates from scratch.

Error: hmmsearch is not found in the HMMER path ! awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading (No such file or directory) Warning: LOC list - is empty.

perl rename_LTR_skim.pl target_sequence.fa LTR_retriever.defalse

Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3

Tue Sep 20 00:58:13 PDT 2022 Warning: The LTR result file has 0 bp!

Tue Sep 20 00:58:13 PDT 2022 Start to find TIR candidates.

Tue Sep 20 00:58:13 PDT 2022 Identify TIR candidates from scratch.

Species: others

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[JiyangChang]

As this issue is listed on the wiki page, so I think it's worth sharing my problem and solution.

I installed EDTA via conda env create -f EDTA.yml and tried to submit my job to compute nodes. However, I always have this Error: The RMblast engine is not installed in RepeatMasker!.

As Shujun and others already mentioned in other threads, this is caused by RepeatMasker error: mdb_env_open: Cannot allocate memory, which sometimes occurred when the software tries to build the index for the input fasta file.

I add the following line in my script and now it solves this issue for me:

export BLASTDB_LMDB_MAP_SIZE=100000000

Hope this could help.

[oushujun]

@JiyangChang Thank you for your suggestion! I have updated the wiki to include your solution. Thanks!

Shujun