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clemgoub / dnaPipeTE

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
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RepeatMasker library #22

Closed nrius closed 1 year ago

nrius commented 5 years ago

Hi!

I am installing dnaPipeTE, following all the steps and including the giri username and subscription. However, I got these errors:

When runnin init.sh:

(...)

Saving to: ‘RepBaseRepeatMaskerEdition-20170127.tar.gz’

RepBaseRepeatMaskerEdition-20170127.tar.gz    100%[===============================================================================================>]   9,43K  --.-KB/s    in 0,03s   

2019-08-06 14:00:44 (296 KB/s) - ‘RepBaseRepeatMaskerEdition-20170127.tar.gz’ saved [9661/9661]

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

##################################################################################################
installation of dependencies done, now run the ./configure script in the ./bin/RepeatMasker folder

And if I continue with the dependencies configuration and then try ./test_config.sh

./test_config.sh 
This is the test script for dnaPipeTE
                  ***                

We will test a few dependancies to be sure tha the pipeline run properly

Testing Java...
java version OK!

Testing RepeatMasker Libraries...
RepeatMasker.lib doesn't include the Repbase sequences! Follow instruction to install RepeatMasker libraries on https://github.com/clemgoub/dnaPipeTE

Do you know how I can solve it? or where the problem may be?

Thanks

clemgoub commented 5 years ago

Hi nrius,

Sorry you are encountering issues with dnaPipeTE. Repbase changed last year to turn into a subscription-based system. Since then, I had not tested how this install works, which can be an issue. In your case it seems that you are downloading something that is not a tar.gz archive. I have to go by the dnaPipeTE script to tell you more.

In the mean time, you can look at the file downloaded: is it a real archive or is it an empty file?

I will come back to you ASAP after I do checks on my side!

Clément

nrius commented 5 years ago

Hi Clément,

Thanks for your prompt answer.

You are right, I copied the file to another directory and tried to extract in. However I got the same result.

tar -xvzf RepBaseRepeatMaskerEdition-20170127.tar.gz gzip: stdin: not in gzip formattar: Child returned status 1tar: Error is not recoverable: exiting now

I downloaded the file from giri and this version can be extracted:

tar -xvzf RepBaseRepeatMaskerEdition-20181026.tar.gz Libraries/Libraries/RMRBSeqs.emblLibraries/README.RMRBSeqs

So I removed the old tar.gz and copied the new one. I configured RepeatMasker and run ./test_config.sh. I still ahve an error, but now it is different:

*./test_config.sh This is the test script for dnaPipeTE ** We will test a few dependancies to be sure tha the pipeline run properlyTesting Java...java version OK!Testing RepeatMasker Libraries...RepeatMasker.lib doesn't include the Repbase sequences! Follow instruction to install RepeatMasker libraries on https://github.com/clemgoub/dnaPipeTE https://github.com/clemgoub/dnaPipeTE

Inside the README.RMRBSeqs I saw that they have changed the libraries. Is this change previous to dnaPipeTE?

COMPATIBILITY WITH OLDER VERSIONS OF REPEATMASKERThis library distribution involves a major shift away from a monolithic( one source ) library format and embraces the notion that libraries mayincreasingly come from multiple sources. Unfortunately this requireschanges in the library structures that will not work with previous versionsof RepeatMasker ( 4.0.6 and earlier ). We have not removed support for older libraries and versions 20140131 and on should continue to work withthe latest releases of RepeatMasker

Thanks,

Nuria

Nuria Rius Camps

El mar., 6 ago. 2019 a las 17:25, Clément Goubert (notifications@github.com) escribió:

Hi nrius,

Sorry you are encountering issues with dnaPipeTE. Repbase changed last year to turn into a subscription-based system. Since then, I had not tested how this install works, which can be an issue. In your case it seems that you are downloading something that is not a tar.gz archive. I have to go by the dnaPipeTE script to tell you more.

In the mean time, you can look at the file downloaded: is it a real archive or is it an empty file?

I will come back to you ASAP after I do checks on my side!

Clément

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFBXY2DNCIVZ2ULON4LQDGJXPA5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3VQORI#issuecomment-518719301, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFADIPILJ35LDEOI7Y3QDGJXPANCNFSM4IJUKAYQ .

nrius commented 5 years ago

Hello again,

I have tried other things that didn't work, but may help you figure out a solution.

In the directory /mypath/dnaPipeTE/bin/RepeatMasker/Libraries, after running init.sh (exiting with gzip error) and configure RepeatMasker I had the following files. I have checked that in RepeatMasker.lib there were 425 sequences, hence trigging the error of test_config.sh

Libraries directory created automatically by init.sh and RM configure:

total 1,6G-rw-r--r-- 1 rius rius 4,3K mag 28 2009 RepeatPeps.readme-rw-r--r-- 1 rius rius 9,9M gen 31 2014 RepeatPeps.lib-rw-r--r-- 1 rius rius 22M ago 7 2015 RepeatAnnotationData.pm-rw-r--r-- 1 rius rius 1,5G set 24 2015 Dfam.hmm-rw-r--r-- 1 rius rius 62M ago 30 2016 taxonomy.dat-rw-r--r-- 1 rius rius 17M gen 29 2017 RMRBMeta.embl-rw-r--r-- 1 rius rius 214 gen 29 2017 README.meta-rw-r--r-- 1 rius rius 208K gen 29 2017 DfamConsensus.embl-rw-rw-r-- 1 rius rius 205K ago 6 15:36 RepeatMaskerLib.embl-rw-rw-r-- 1 rius rius 127K ago 6 15:36 RepeatMasker.lib-rw-rw-r-- 1 rius rius 5,2K ago 6 15:37 RepeatMasker.lib.nin-rw-rw-r-- 1 rius rius 43K ago 6 15:37 RepeatMasker.lib.nhr-rw-rw-r-- 1 rius rius 28K ago 6 15:37 RepeatMasker.lib.nsq-rw-rw-r-- 1 rius rius 9,1M ago 6 15:37 RepeatPeps.lib.psq-rw-rw-r-- 1 rius rius 83K ago 6 15:37 RepeatPeps.lib.pin-rw-rw-r-- 1 rius rius 1,5M ago 6 15:37 RepeatPeps.lib.phr

I looked at this directory from a previous version ( v.1.2_04-2016 ) a colleague had, and copied the content into the /Libraries directory. I thought this was unlikely to work as the RepeatMasker library should be the same verison of RepeatMasker. Anyway, now the RepeatMasker.lib in the library directory has 35996 sequences, but the test_config.sh error is triggered all the same, and don't know why.

total 1,8G

-rwxr-xr-x 1 root root 96M ago 7 17:08 RepeatMasker.lib-rwxr-xr-x 1 root root 137M ago 7 17:08 RepeatMaskerLib.embl-rw-r--r-- 1 root root 4,6M ago 7 17:08 RepeatMasker.lib.nhr-rw-r--r-- 1 root root 422K ago 7 17:08 RepeatMasker.lib.nin-rw-r--r-- 1 root root 24M ago 7 17:08 RepeatMasker.lib.nsq-rwxr-xr-x 1 root root 3,6K ago 7 17:08 README-rwxr-xr-x 1 root root 1,5G ago 7 17:08 Dfam.hmm-rwxr-xr-x 1 root root 62M ago 7 17:08 taxonomy.dat-rwxr-xr-x 1 root root 22M ago 7 17:08 RepeatAnnotationData.pm-rwxr-xr-x 1 root root 9,9M ago 7 17:08 RepeatPeps.lib-rw-r--r-- 1 root root 1,5M ago 7 17:08 RepeatPeps.lib.phr-rw-r--r-- 1 root root 83K ago 7 17:08 RepeatPeps.lib.pin-rw-r--r-- 1 root root 9,1M ago 7 17:08 RepeatPeps.lib.psq-rwxr-xr-x 1 root root 4,3K ago 7 17:08 RepeatPeps.readme

I hope this can help you somehow to understand what is happening. Thanks,

Nuria

Nuria Rius Camps

El mar., 6 ago. 2019 a las 18:11, Nuria Rius (nuria.rius.camps@gmail.com) escribió:

Hi Clément,

Thanks for your prompt answer.

You are right, I copied the file to another directory and tried to extract in. However I got the same result.

tar -xvzf RepBaseRepeatMaskerEdition-20170127.tar.gz gzip: stdin: not in gzip formattar: Child returned status 1tar: Error is not recoverable: exiting now

I downloaded the file from giri and this version can be extracted:

tar -xvzf RepBaseRepeatMaskerEdition-20181026.tar.gz Libraries/Libraries/RMRBSeqs.emblLibraries/README.RMRBSeqs

So I removed the old tar.gz and copied the new one. I configured RepeatMasker and run ./test_config.sh. I still ahve an error, but now it is different:

*./test_config.sh This is the test script for dnaPipeTE ** We will test a few dependancies to be sure tha the pipeline run properlyTesting Java...java version OK!Testing RepeatMasker Libraries...RepeatMasker.lib doesn't include the Repbase sequences! Follow instruction to install RepeatMasker libraries on https://github.com/clemgoub/dnaPipeTE https://github.com/clemgoub/dnaPipeTE

Inside the README.RMRBSeqs I saw that they have changed the libraries. Is this change previous to dnaPipeTE?

COMPATIBILITY WITH OLDER VERSIONS OF REPEATMASKERThis library distribution involves a major shift away from a monolithic( one source ) library format and embraces the notion that libraries mayincreasingly come from multiple sources. Unfortunately this requireschanges in the library structures that will not work with previous versionsof RepeatMasker ( 4.0.6 and earlier ). We have not removed support for older libraries and versions 20140131 and on should continue to work withthe latest releases of RepeatMasker

Thanks,

Nuria

Nuria Rius Camps

El mar., 6 ago. 2019 a las 17:25, Clément Goubert (< notifications@github.com>) escribió:

Hi nrius,

Sorry you are encountering issues with dnaPipeTE. Repbase changed last year to turn into a subscription-based system. Since then, I had not tested how this install works, which can be an issue. In your case it seems that you are downloading something that is not a tar.gz archive. I have to go by the dnaPipeTE script to tell you more.

In the mean time, you can look at the file downloaded: is it a real archive or is it an empty file?

I will come back to you ASAP after I do checks on my side!

Clément

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFBXY2DNCIVZ2ULON4LQDGJXPA5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3VQORI#issuecomment-518719301, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFADIPILJ35LDEOI7Y3QDGJXPANCNFSM4IJUKAYQ .

clemgoub commented 5 years ago

Hi Nuria, Sorry for my late reply, I am currently traveling. It is possible that the new libraries does not work with this config script while being effectively installed. If you did the RM install following the instructions and this did not return any error, you might have the libraries effe installed. Did you try to run dnaPipeTE anyways?

Clément

nrius commented 5 years ago

Hi Clément,

Sorry for the late reply, I have been trying different solutions. I got dnaPipeTE installed on a cluster I have access and this time the run with the test files exited successfully. However, the Counts.txt file showed there was no classification per Superfamilies (see below) and probably because of that the pie chart was not done. I thought it could be because of low coverage and I've tried with my human data using different combinations. The first result I've got so far, with 4 million reads and 3 samplings, yielded a similar Counts.txt file (see below). Do you know if this indicates a problem with the libraries or something else? Is there something I can check?

Thanks for your help Nuria

------Test-------

LTR 0 LINE 0 SINE 0 DNA 0 MITE 0 Helitron 0 rRNA 0 Low_Complexity 0 Satellite 0 Tandem_repeats 0 Simple_repeat 0 others 0 na 0 Others 0 Total 987936

-------human data------------------ LTR 0 LINE 0 SINE 0 DNA 0 MITE 0 Helitron 0 rRNA 0 Low_Complexity 0 Satellite 0 Tandem_repeats 0 Simple_repeat 0 others 0 na 0 Others 0 Total 596461348

Nuria Rius Camps

El mié., 7 ago. 2019 a las 22:47, Clément Goubert (notifications@github.com) escribió:

Hi Nuria, Sorry for my late reply, I am currently traveling. It is possible that the new libraries does not work with this config script while being effectively installed. If you did the RM install following the instructions and this did not return any error, you might have the libraries effe installed. Did you try to run dnaPipeTE anyways?

Clément

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFB767ZS73NZIJ7ARGLQDMYF3A5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ZVEOA#issuecomment-519262776, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFBJYYV2ZNGZQFMAJB3QDMYF3ANCNFSM4IJUKAYQ .

clemgoub commented 5 years ago

Hi Nuria,

Glad you made some progress with the install. What you think is very likely. Can you verify the syntax in your repbase fasta file? The format of the header must be:

>RepeatName#Class/subclass

the # is very important, and the Class and subclass names must be present in the file new_list_of_RM_superclass_colors_sortedOK present in your dnaPipeTE folder.

Let me know if this helped,

Cheers,

Clément

nrius commented 5 years ago

Hi Clément, In "dnaPipeTE/bin/RepeatMasker/Libraries/RepeatMasker.lib" the header is the expected one, this is an example: ">FordP_Test-1N2#DNA/hAT-Tip100 [S:] " . "dnaPipeTE/new_list_of_RM_superclass_colors_sortedOK" is the same as the one in your GitHub.

Could it be something else?

Thanks,

Nuria

Nuria Rius Camps

El mar., 3 sept. 2019 a las 15:36, Clément Goubert (< notifications@github.com>) escribió:

Hi Nuria,

Glad you made some progress with the install. What you think is very likely. Can you verify the syntax in your repbase fasta file? The format of the header must be:

RepeatName#Class/subclass

the # is very important, and the Class and subclass names must be present in the file new_list_of_RM_superclass_colors_sortedOK present in your dnaPipeTE folder.

Let me know if this helped,

Cheers,

Clément

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFG4BVCGOQSUXFBWQP3QHZR7RA5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5YG2SA#issuecomment-527461704, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFBL74VAEUHS556NNG3QHZR7RANCNFSM4IJUKAYQ .

clemgoub commented 5 years ago

Hi!

If I understand correctly you never had a pieChard and Counts working, even with a test run with test data right?

Clém

nrius commented 5 years ago

Exactly. Although when dnaPipeTE finishes it doesn't give errors:

Drawing graphs... Done Removing Trinity runs files... done Finishin time: Mon Sep 2 20:13:41 2019 ########################

see you soon !!!

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

El mié., 4 sept. 2019 17:34, Clément Goubert notifications@github.com escribió:

Hi!

If I understand correctly you never had a pieChard and Counts working, even with a test run with test data right?

Clém

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFCE3N35VINIUWZPHHLQH7IR5A5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD537SEQ#issuecomment-527956242, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFAVTW33YWWQAEKPLNLQH7IR5ANCNFSM4IJUKAYQ .

clemgoub commented 5 years ago

I see... Can you send me your whole logs and command?

nrius commented 5 years ago

Sure, Here are the commands and the logs for the test run (dnaPipeTE_2.job and nr_dna_5_2.o796095) and the run with my data (dnaPipeTE_5_2.job and nr_dna_5_2.o796095).

Thanks Nuria

Nuria Rius Camps

El jue., 5 sept. 2019 a las 15:02, Clément Goubert (< notifications@github.com>) escribió:

I see... Can you send me your whole logs and command?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFBQB6DEUR6UH3RUUPLQID7MXA5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD57AJLI#issuecomment-528352429, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFATXJPBB6XORFA4FSTQID7MXANCNFSM4IJUKAYQ .

clemgoub commented 5 years ago

Hi,

I'm sorry, I didn't get the files. You can email them to me at cg629 @ cornell.edu

nrius commented 5 years ago

Hi Clément, let me know if you still have problems to download them.

Thanks

Nuria Rius Camps

El vie., 6 sept. 2019 a las 15:48, Clément Goubert (< notifications@github.com>) escribió:

Hi,

I'm sorry, I didn't get the files. You can email them to me at cg629 @ cornell.edu

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/clemgoub/dnaPipeTE/issues/22?email_source=notifications&email_token=AKBPMFHKGIXQZ3JHDAHJ533QIJNTVA5CNFSM4IJUKAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6C4WXI#issuecomment-528862045, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBPMFEVCN4NC3MBIXA2MYTQIJNTVANCNFSM4IJUKAYQ .

clemgoub commented 5 years ago

Yes I'm sorry I didn't got anything...

nrius commented 5 years ago

Hi, Do you mean you don't understand why this happened or that you didn't receive the files?

Thanks anyway,

Nuria

Nuria Rius Camps

El lun., 9 sept. 2019 a las 15:28, Clément Goubert (< notifications@github.com>) escribió:

Yes I'm sorry I didn't got anything...

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jcerca commented 3 years ago

Dear Clément and Nuria,

dnaPipeTE seems like a wonderful pipeline - I am really looking forward to installing it and getting it running as part of my work.

Not sure if you ever got to solve this, but I did, so posting it so it is available to everyone.

This was the error I got

2020-12-19 22:01:46 (132 MB/s) - ‘RepBaseRepeatMaskerEdition-20170127.tar.gz’ saved [9661/9661]
gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

When I find this file, it seems empty:

find . | grep RepBaseRepeatMaskerEdition-20170127.tar.gz
 ./bin/RepeatMasker/RepBaseRepeatMaskerEdition-20170127.tar.gz

ls -lah  ./bin/RepeatMasker/RepBaseRepeatMaskerEdition-20170127.tar.gz
-rwxrwxrwx 1 josepc posixgroup 9.5K Mar 21  2019 RepBaseRepeatMaskerEdition-20170127.tar.gz

tar xvzf  ./bin/RepeatMasker/RepBaseRepeatMaskerEdition-20170127.tar.gz
gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

So then I googled: "RepBaseRepeatMaskerEdition-20170127.tar.gz" and came with the following link: https://github.com/yjx1217/RMRB

& did the following:

cd ./bin/RepeatMasker
wget https://github.com/yjx1217/RMRB/raw/master/RepBaseRepeatMaskerEdition-20170127.tar.gz ## obtained from the URL above
mv RepBaseRepeatMaskerEdition-20170127.tar.gz.1 RepBaseRepeatMaskerEdition-20170127.tar.gz  # I do this since wget generated a "*.1" file.

This did not work, so I tried understanding what init.sh was doing with the repeatmask library.

cd ../../
grep gz init.sh
###grep result
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
curl -k -L  ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-x64-linux.tar.gz -o ncbi-rmblastn-2.2.28-x64-linux.tar.gz
tar -xvf ncbi-rmblastn-2.2.28-x64-linux.tar.gz
rm ncbi-rmblastn-2.2.28-x64-linux.tar.gz
curl -k -L ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-x64-linux.tar.gz -o ncbi-blast-2.2.28+-x64-linux.tar.gz
tar -xvf ncbi-blast-2.2.28+-x64-linux.tar.gz
rm ncbi-blast-2.2.28+-x64-linux.tar.gz
curl -k -L http://repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz -o RepeatMasker-open-4-0-7.tar.gz
tar -xvf RepeatMasker-open-4-0-7.tar.gz
wget http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz --password=$GIRINST_PASSWORD  --user=$GIRINST_USERNAME
mv RepBaseRepeatMaskerEdition-20170127.tar.gz RepeatMasker/
tar -zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz

This tells me that it downloads it everytime I run the bash ./init.sh command. So I basically used nano and literally replaced the line:

wget http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz --password=$GIRINST_PASSWORD  --user=$GIRINST_USERNAME

with:

wget https://github.com/yjx1217/RMRB/raw/master/RepBaseRepeatMaskerEdition-20170127.tar.gz

and it worked. I still have some trinity issues, though - hoping to solve it soon.

clemgoub commented 3 years ago

Dear José,

I'm sorry for the delays. I recently moved from the US to Canada and cannot provide a very fast support on dnaPipeTE at the moment... Unfortunately, dnaPipeTE needs a big update... In the meantime, please DM me if you have problems with Trinity. Best,

Clément

jcerca commented 3 years ago

Hi Clément,

thank you for your answer. I managed to solve it.. was pointing out to the wrong perl/lib/path - newbie mistake!

Looking forward to see that update. TEs are a fascinating part of genomics and I hope to answer many fascinating questions with dnaPipeTE :)

Best, José