RepeatMasker libraries not found

[caroliog]

Hi!

I'm attempting to install your program, but when configuring RepeatMasker it doesn't seem to find the required libraries. I'm pointing to a path that should contain them, but I get this error message:

No repeat libraries found!  At a minimum the Dfam_consensus
is required to run.  Please download and install the latest 
Dfam_consensus.  It is highly recommended that you also install the
latest RepBase RepeatMasker Edition library obtainable from GIRI.
General instructions can be found here: http://www.repeatmasker.org

The folder does have a file called DfamConsensus.embl, but is this not what it is looking for?

Thanks so much for any help!

Caroline

[clemgoub]

Hi Caroline,

Can you tell me exactly which path you are giving RepeatMasker for the libraries? Normally, the directory to point to is dnaPipeTE/bin/RepeatMasker/Libraries To double check, follow the instruction to install the RM libraries here: http://repeatmasker.org/RepeatMasker/ update the DFAM library as indicated:

wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz
gunzip Dfam.h5.gz
mv Dfam.h5 <installpath>/dnaPipeTE/bin/RepeatMasker/Libraries
cd <installpath>/dnaPipeTE/bin/RepeatMasker/
./configure

Please let me know if the libraries are still not working, I will find another solution!

Cheers,

Clément

[caroliog]

Hi,

Thank you for responding!

I’ve updated the the DFAM library as indicated, but running ./test_config.sh still tells me

RepeatMasker.lib doesn't include the Repbase sequences!

The path I give for RepeatMasker is /proj/sllstore2017073/private/Caroline/dnaPipeTE/bin/RepeatMasker (where /proj/sllstore2017073/private/Caroline is my work directory) during the configuration process I am never actually asked specifically for the path to the libraries, but I'm assuming it looks in /proj/sllstore2017073/private/Caroline/dnaPipeTE/bin/RepeatMasker/Libraries/ where Dfam.h5 is located.

Caroline

[clemgoub]

Hello Caroline,

I think it can still works. The test script only look for Repbase libraries, but these DFAM should work just as well with dnaPipeTE. I suggest you to do the test run as indicated in the GitHub, regardless this error message.

Let me know if you have results, and you can send me the full log and command line if it doesn't go through.

Best,

Clément

[nishmadahal]

Hello,

I ran ./init.sh Now I am supposed to find "cd bin/RepeatMasker" and run "./configure"

But, i only have directory named "parallel" inside bin

I found RepBaseRepeatMaskerEdition-20170127.tar.gz outside bin, but it cannot be unzipped.

2021-02-25 15:29:32 (18.8 MB/s) - ‘RepBaseRepeatMaskerEdition-20170127.tar.gz.2’ saved [9661/9661]

mv: cannot move 'RepBaseRepeatMaskerEdition-20170127.tar.gz' to 'RepeatMasker/': Not a directory ./init.sh: line 69: cd: RepeatMasker: No such file or directory

gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is not recoverable: exiting now

[clemgoub]

Hello,

It seems that the download and extraction or RepeatMasker (step before) did not work. I tried this morning and the RepeatMasker folder should be in ./bin after running the script.

I advise you to try manually from within the dnaPipeTE folder:

cd bin/
curl -k -L http://repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz -o RepeatMasker-open-4-0-7.tar.gz
tar -zxvf RepeatMasker-open-4-0-7.tar.gz

after that, your Repbase library seems to have an extra ".2" at the end. Simply

mv RepBaseRepeatMaskerEdition-20170127.tar.gz.2 bin/RepeatMasker/RepBaseRepeatMaskerEdition-20170127.tar.gz
cd bin/RepeatMasker
tar -zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz

now you can run ./configure to finalize RepeatMasker installation I assume that you have a Repbase subscription. If not, follow the instruction to use the DFAM libraries as indicated here: http://www.repeatmasker.org/RepeatMasker/

Let me know how it works for you, and please let me know if you need further help!

Cheers,

Clément

[nishmadahal]

Thanks, for prompt response.

Looks like RepeatMasker-open-4-0-7.tar.gz is not a gzip file. So, how do I unzip it? gzip -v -t RepeatMasker-open-4-0-7.tar.gz

gzip: RepeatMasker-open-4-0-7.tar.gz: not in gzip format

Also, I have my profile on Repbase (whose user id and password I provided in "init.sh" ), but I do not have a subscription. I was also struggling to find DFAm libraries. Thanks for your help.

Many thanks Nishma Dahal DST- INSPIRE faculty & Asst. Professor (AcSIR), Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP)

On Thu, Feb 25, 2021 at 7:01 PM Clément Goubert notifications@github.com wrote:

Hello,

It seems that the download and extraction or RepeatMasker (step before) did not work. I tried this morning and the RepeatMasker folder should be in ./bin after running the script.

I advise you to try manually from within the dnaPipeTE folder:

cd bin/

curl -k -L http://repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz -o RepeatMasker-open-4-0-7.tar.gz

tar -zxvf RepeatMasker-open-4-0-7.tar.gz

after that, your Repbase library seems to have an extra ".2" at the end. Simply

mv RepBaseRepeatMaskerEdition-20170127.tar.gz.2 bin/RepeatMasker/RepBaseRepeatMaskerEdition-20170127.tar.gz

cd bin/RepeatMasker

tar -zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz

now you can run ./configure to finalize RepeatMasker installation I assume that you have a Repbase subscription. If not, follow the instruction to use the DFAM libraries as indicated here: http://www.repeatmasker.org/RepeatMasker/

Let me know how it works for you, and please let me know if you need further help!

Cheers,

Clément

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[clemgoub]

To unzip it, you need to use the tar+gzip command

tar -zxvf RepeatMasker-open-4-0-7.tar.gz

Cheers,

Clément

[nishmadahal]

Somehow thats not working. It gives me following error gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is not recoverable: exiting now

Nishma Dahal DST- INSPIRE faculty & Asst. Professor (AcSIR), Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP)

On Fri, Feb 26, 2021 at 8:06 PM Clément Goubert notifications@github.com wrote:

To unzip it, you need to use the tar+gzip command

tar -zxvf RepeatMasker-open-4-0-7.tar.gz

Cheers,

Clément

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[clemgoub]

Ho, then it could be that the downloaded file is corrupted.

You can try the following:

cd in the dnaPipTE/bin directory

wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.1.tar.gz
gunzip RepeatMasker-4.1.1.tar.gz
tar xvf RepeatMasker-4.1.1.tar

This should download and unpack the latest RepeatMasker version. The next step is to configure it:

cd ./RepeatMasker
./configure

Enter path [ /usr/local/bin/perl ]:

Just press enter. The path should be found automatically.

Enter path [ /yourpath/dnaPipeTE/bin/RepeatMasker ]:

Same thing here, the path to RepeatMasker should be found automatically.

Enter path [ ]: </yourpath>/dnaPipeTE/bin/trf

Here, replace by the path to the dnaPipeTE folder. The default prompt should be empty, unless you already have trf in your path.

Add a Search Engine:
   1. CrossMatch: [ Un-configured ]
   2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]
   3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
   4. HMMER3.1 & DFAM: [ Un-configured ]

   5. Done

Enter Selection: 2

Choose 2 and press enter

**RMBlast (rmblastn) INSTALLATION PATH**

This is the path to the location wherethe rmblastn and makeblastdb programs can be found.

Enter path [  ]: </yourpath>/dnaPipeTE/bin/ncbi-blast-2.2.28+/bin  

Same thing here, replace with the path to your local installation of dnaPipeTE. Then press enter. Be carefull to not add a final / after the 'bin', for some reason it is very sensitive!

Do you want RMBlast to be your default
search engine for Repeatmasker? (Y/N)  [ Y ]:Y

Choose Y and press enter.

Add a Search Engine:
   1. CrossMatch: [ Un-configured ]
   2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]
   3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
   4. HMMER3.1 & DFAM: [ Un-configured ]

   5. Done

Enter Selection: 5

Choose 5 here and press enter.

This should install RepeatMasker and build the default libraries (DFAM). Let me know if you need further assistance!

Best,

Clément

[nishmadahal]

Hi sorry again I am stuck. I downloaded it manually (coz institute's internet was blocking it when I used wget) and unzipped repeatmasker, then gunzip and tar xvf worked. I am now trying to configure, I entered perl path.

I am stuck after this; This is what I get after I put dnaPipe folder The full path including the name for the TRF program.TRF_PRGM: /home/user/Downloads/dnaPipeTE-masterThe value "/home/user/Downloads/dnaPipeTE-master" appears to be a directory ratherthan an executable binary or script!<PRESS ENTER TO CONTINUE, CTRL-C TO BREAK>

Inside my dnaPipe folder I have the following;

user@user:~/Downloads/dnaPipeTE-master/bin/RepeatMasker$ ls addRepBase.pl INSTALL RepeatMaskerConfig.pm ArrayListIterator.pm Libraries repeatmasker.help ArrayList.pm LibraryUtils.pm RepeatProteinMask bluegrad.jpg LICENSE RepeatRecord.pm configure Matrices SearchEngineI.pm CrossmatchSearchEngine.pm Matrix.pm SearchResultCollection.pm DateRepeats NCBIBlastSearchEngine.pm SearchResult.pm daterepeats.help NCBIBlastXSearchEngine.pm SeqDBI.pm DFAM.pm ProcessRepeats SimpleBatcher.pm DFAMRecord.pm PRSearchResult.pm Taxonomy.pm DupMasker PubRef.pm TRF.pm EMBL.pm README.md TRFResult.pm famdb.py ReleaseNotes TRFSearchResult.pm FastaDB.pm RepbaseEMBL.pm util HMMERSearchEngine.pm RepbaseRecord.pm WUBlastSearchEngine.pm HTMLAnnotHeader.html RepeatMasker WUBlastXSearchEngine.pm

Here, replace by the path to the dnaPipeTE folder. The default prompt should be empty, unless you already have trf in your path.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 2

Choose 2 and press enter

RMBlast (rmblastn) INSTALLATION PATH

This is the path to the location wherethe rmblastn and makeblastdb programs can be found.

Enter path [ ]: /dnaPipeTE/bin/ncbi-blast-2.2.28+/bin

Same thing here, replace with the path to your local installation of dnaPipeTE. Then press enter. Be carefull to not add a final / after the 'bin', for some reason it is very sensitive!

Do you want RMBlast to be your default

search engine for Repeatmasker? (Y/N) [ Y ]:Y

Choose Y and press enter.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 5

Choose 5 here and press enter.

This should install RepeatMasker and build the default libraries (DFAM).

Nishma Dahal DST- INSPIRE faculty & Asst. Professor (AcSIR), Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP)

On Fri, Feb 26, 2021 at 11:45 PM Clément Goubert notifications@github.com wrote:

Ho, then it could be that the downloaded file is corrupted.

You can try the following:

cd in the dnaPipTE/bin directory

wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.1.tar.gz

gunzip RepeatMasker-4.1.1.tar.gz

tar xvf RepeatMasker-4.1.1.tar

This should download and unpack the latest RepeatMasker version. The next step is to configure it:

cd ./RepeatMasker

./configure

Enter path [ /usr/local/bin/perl ]:

Just press enter. The path should be found automatically.

Enter path [ /yourpath/dnaPipeTE/bin/RepeatMasker ]:

Same thing here, the path to RepeatMasker should be found automatically.

Enter path [ ]: /dnaPipeTE/bin/trf

Here, replace by the path to the dnaPipeTE folder. The default prompt should be empty, unless you already have trf in your path.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 2

Choose 2 and press enter

RMBlast (rmblastn) INSTALLATION PATH

This is the path to the location wherethe rmblastn and makeblastdb programs can be found.

Enter path [ ]: /dnaPipeTE/bin/ncbi-blast-2.2.28+/bin

Same thing here, replace with the path to your local installation of dnaPipeTE. Then press enter. Be carefull to not add a final / after the 'bin', for some reason it is very sensitive!

Do you want RMBlast to be your default

search engine for Repeatmasker? (Y/N) [ Y ]:Y

Choose Y and press enter.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 5

Choose 5 here and press enter.

This should install RepeatMasker and build the default libraries (DFAM). Let me know if you need further assistance!

Best,

Clément

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[nishmadahal]

Hello again

We have tried to resolve some of the basic issues and finally reached the step to run the test script provided. Please find attached the log of the error.

Many thanks Nishma Dahal DST- INSPIRE faculty & Asst. Professor (AcSIR), Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP)

On Mon, Mar 1, 2021 at 11:48 AM Nishma Dahal dahal.nishma@gmail.com wrote:

Hi sorry again I am stuck. I downloaded it manually (coz institute's internet was blocking it when I used wget) and unzipped repeatmasker, then gunzip and tar xvf worked. I am now trying to configure, I entered perl path.

I am stuck after this; This is what I get after I put dnaPipe folder The full path including the name for the TRF program.TRF_PRGM: /home/user/Downloads/dnaPipeTE-masterThe value "/home/user/Downloads/dnaPipeTE-master" appears to be a directory ratherthan an executable binary or script!<PRESS ENTER TO CONTINUE, CTRL-C TO BREAK>

Inside my dnaPipe folder I have the following;

user@user:~/Downloads/dnaPipeTE-master/bin/RepeatMasker$ ls addRepBase.pl INSTALL RepeatMaskerConfig.pm ArrayListIterator.pm Libraries repeatmasker.help ArrayList.pm LibraryUtils.pm RepeatProteinMask bluegrad.jpg LICENSE RepeatRecord.pm configure Matrices SearchEngineI.pm CrossmatchSearchEngine.pm Matrix.pm SearchResultCollection.pm DateRepeats NCBIBlastSearchEngine.pm SearchResult.pm daterepeats.help NCBIBlastXSearchEngine.pm SeqDBI.pm DFAM.pm ProcessRepeats SimpleBatcher.pm DFAMRecord.pm PRSearchResult.pm Taxonomy.pm DupMasker PubRef.pm TRF.pm EMBL.pm README.md TRFResult.pm famdb.py ReleaseNotes TRFSearchResult.pm FastaDB.pm RepbaseEMBL.pm util HMMERSearchEngine.pm RepbaseRecord.pm WUBlastSearchEngine.pm HTMLAnnotHeader.html RepeatMasker WUBlastXSearchEngine.pm

Here, replace by the path to the dnaPipeTE folder. The default prompt should be empty, unless you already have trf in your path.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 2

Choose 2 and press enter

RMBlast (rmblastn) INSTALLATION PATH

This is the path to the location wherethe rmblastn and makeblastdb programs can be found.

Enter path [ ]: /dnaPipeTE/bin/ncbi-blast-2.2.28+/bin

Same thing here, replace with the path to your local installation of dnaPipeTE. Then press enter. Be carefull to not add a final / after the 'bin', for some reason it is very sensitive!

Do you want RMBlast to be your default

search engine for Repeatmasker? (Y/N) [ Y ]:Y

Choose Y and press enter.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 5

Choose 5 here and press enter.

This should install RepeatMasker and build the default libraries (DFAM).

Nishma Dahal DST- INSPIRE faculty & Asst. Professor (AcSIR), Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP)

On Fri, Feb 26, 2021 at 11:45 PM Clément Goubert notifications@github.com wrote:

Ho, then it could be that the downloaded file is corrupted.

You can try the following:

cd in the dnaPipTE/bin directory

wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.1.tar.gz

gunzip RepeatMasker-4.1.1.tar.gz

tar xvf RepeatMasker-4.1.1.tar

This should download and unpack the latest RepeatMasker version. The next step is to configure it:

cd ./RepeatMasker

./configure

Enter path [ /usr/local/bin/perl ]:

Just press enter. The path should be found automatically.

Enter path [ /yourpath/dnaPipeTE/bin/RepeatMasker ]:

Same thing here, the path to RepeatMasker should be found automatically.

Enter path [ ]: /dnaPipeTE/bin/trf

Here, replace by the path to the dnaPipeTE folder. The default prompt should be empty, unless you already have trf in your path.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 2

Choose 2 and press enter

RMBlast (rmblastn) INSTALLATION PATH

This is the path to the location wherethe rmblastn and makeblastdb programs can be found.

Enter path [ ]: /dnaPipeTE/bin/ncbi-blast-2.2.28+/bin

Same thing here, replace with the path to your local installation of dnaPipeTE. Then press enter. Be carefull to not add a final / after the 'bin', for some reason it is very sensitive!

Do you want RMBlast to be your default

search engine for Repeatmasker? (Y/N) [ Y ]:Y

Choose Y and press enter.

Add a Search Engine:

1. CrossMatch: [ Un-configured ]

2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]

3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]

4. HMMER3.1 & DFAM: [ Un-configured ]

5. Done

Enter Selection: 5

Choose 5 here and press enter.

This should install RepeatMasker and build the default libraries (DFAM). Let me know if you need further assistance!

Best,

Clément

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[clemgoub]

Hi Nishma,

I'm sorry I didn't get the log file!

Clément

[nishmadahal]

Hi

The error message I get is (also attached),

----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) --

CMD: /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 1 -m 25 -s 100000000 --canonical single.fa /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/util/..//trinity-plugins/jellyfish/bin/jellyfish: error: `/home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/jellyfish/bin/.libs/jellyfish' does not exist This script is just a wrapper for jellyfish. See the libtool documentation for more information. Error, cmd: /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 1 -m 25 -s 100000000 --canonical single.fa died with ret 256 at /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/util/ insilico_read_normalization.pl line 758. Error, cmd: /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/util/ insilico_read_normalization.pl --seqType fa --JM 10G --max_cov 50 --CPU 1 --output /home/user/Downloads/dnaPipeTE-master/Test_output/Trinity_run2/insilico_read_normalization --max_pct_stdev 10000 --single /home/user/Downloads/dnaPipeTE-master/Test_output/s1_test_dataset.fastq.fasta died with ret 512 at /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/Trinity line 2544. main::process_cmd("/home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trini"...) called at /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/Trinity line 3090 main::normalize("/home/user/Downloads/dnaPipeTE-master/Test_output/Trinity_run"..., 50, ARRAY(0x55f47c939e10)) called at /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/Trinity line 3037 main::run_normalization(50, ARRAY(0x55f47c939e10)) called at /home/user/Downloads/dnaPipeTE-master/bin/trinityrnaseq-Trinity-v2.5.1/Trinity line 1302 RepeatMasker version 4.1.1 Search Engine: NCBI/RMBLAST [ 2.10.0+ ]

Using Master RepeatMasker Database: /home/user/Downloads/dnaPipeTE-master/bin/RepeatMasker/Libraries/RepeatMaskerLib.h5 Title : Dfam Version : 3.2 Date : 2020-07-02 Families : 6,953

Species/Taxa Search: [NCBI Taxonomy ID: ]

0 families in ancestor taxa; 6953 lineage-specific families

Many thanks Nishma Dahal DST- INSPIRE faculty & Asst. Professor (AcSIR), Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur-176061 (HP)

On Thu, Mar 4, 2021 at 9:47 PM Clément Goubert notifications@github.com wrote:

Hi Nishma,

I'm sorry I didn't get the log file!

Clément

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[clemgoub]

Hi Nishma,

It seems that the install of Trinity was incomplete, and Jellyfhish (count k-mers) is not installed. You can try to re-install Trinity

cd /home/user/Downloads/dnaPipeTE-master/bin
rm -r trinityrnaseq-Trinity-v2.5.1
curl -k -L https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.5.1.tar.gz -o Trinity-v2.5.1.tar.gz
tar -zxvf Trinity-v2.5.1.tar.gz
cd trinityrnaseq-Trinity-v2.5.1
make

Look for possible errors during the compilation, especially regarding Jellyfish, and let me know. If the install goes without errors, you can try the test run of dnaPipeTE again.

Cheers,

Clément

[clemgoub]

Closing this issue since it concerns the non-container version. Please DM if further support is needed. Thank you!