Installation issues starting with Trinity [SOLVED]

Page 1 of 2 1, 2  Next

View previous topic View next topic Go down

Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Tue Jan 05, 2016 2:36 pm

Here is some email exchanges about some issues occurring during the set-up of dnaPipeTE, starting with a problem with Trinity:

I am currently trying to use dnaPipeTE but I am having a little difficulties, I was wondering if there was anyway you could help.

so I start running the program and it starts running and creating the sample files but it hits a "fatal error"

awk: cmd. line:1: fatal: cannot open file `/home/lblancob/testDNApipe/Trinity_run0/chrysalis/readsToComponents.out.sort' for reading (No such file or directory)
Done

and it also creates trinty folders that are empty. do you have any idea what can I do?


Yes, it seems that Trinity doesn’t work properly. Could you send me the whole log file for dnaPipeTE that I have a look at the Trinity behaviour ?
Which version of Trinity do you use ?

I think it is a Java issue with Trinity

"Error, Trinity requires access to Java version 1.6 or 1.7.  Currently installed version is:  at /lustre/work/apps/trinityrnaseq_r20131110/Trinity.pl line 665."

Try to upgrade your java installation to >= 1.6 and it should work !


So trinity worked, but now it wont give me any graphs, attach is the log.
and there error that gave me is this. ...


Code:
Drawing graphs...
/bin/sh: /lustre/work/daray/software/dnaPipeTE/graph.R: /usr/bin/Rscript: bad interpreter: No such file or directory
Done
Finishin time: Mon Apr  6 09:15:19 2015
########################
#   see you soon !!!   #
########################




- Is there a « Trinity.fasta.out » file in the output folder ? Because there was a « cat » error on this, and thus the following step couldn’t run properly. It is possible that RepeatMasker didn’t work well (I had some troubles with it…)
- Is there a Trinity.fasta file (sign that Trinity worked properly), and if yes, is it not empty ?

Then, I also saw an error maybe related to GNU Parallel. Is it well installed ?
I am also wondering what kind of machine are you using to run dnaPipeTE ? If you use a cluster, do you run it on multiple nodes/machine ? I designed it to run with several cores but I did not test if it works with several cores dispatched on different machines.

Finally, the error you report about one of the last R script could be due to a mistake in the code, could you send me the « dnaPipeTE.py » file you use that I check it is ok ?


I can see several trinity files but not trinity.fasta.out. there is a trinity.fasta and it is not empty.
I am working on clusters. how would you commend me to run the program to avoid errors?

I will check the parallel installation also.


Ok, so Trinity is working well, it seems that the main problem is with RepeatMasker, I think I got it:

in the config.ini file, it seems you just gave the path to the folder for repeat masker, not to the executable. In the log:
"/bin/sh: /lustre/work/daray/software/RepeatMasker: is a directory »

try to change it to /lustre/work/daray/software/RepeatMasker/RepeatMasker

So I think this is why RM didn’t worked and you do not have the Trinity.fasta.out and the following couldn’t work properly.

Concerning the use on the cluster, you can run it using multiple cores but try to use one only node/machine (to be sure that GNU Parallel is well configured).


It looks ok for me, could you test that R and the command /usr/bin/Rscript are working well on your cluster ?
Maybe the Rscript command is not in /usr/bin/ but I think it is the default installation of R.


I will make all the changes you suggested and will run a test run. I will let you know how it works.


so this is the latest issue with TEpipe

1. I have made all the changes you suggested (repeatmasker, R version, and I am using only one node) and after this there is still a fatal error in line1: (although the program keeps running dispite this erros)
2. no trinity.fasta.out file is created
3. whe I look at the annotation files it is empty, I assume (like you said before) step 1 is not working anything beyond that won't work either
4. along that line it says that several files are empty.


can you think about anything else I could be doing wrong?


You’re right, while RepeatMasker doesn’t work, the next step won’t run properly.
It appears that your path to RepeatMasker is still wrong:

/bin/sh: /lustre/work/daray/software/RepeatMasker-4.03/RepeatMasker: No such file or directory

I think the other things are ok, there is no more the issue with parallel so that is OK for the next steps !



One last question!
if I want to run dnaPipeTE in Read1 and Read2 how would I set the script up?
I have been trying to put (example)

dnaPipeTE.py -input Read1.fastq Read2.fastq -output Read1and2_TE_OUT  ....

and it does not run



Unfortunately dnaPipeTE do not handle paired-end yet. I found during development that sometimes using paired-end during assembly of TEs could cause chimerism (especially if TEs are the one inside the others or at high density), thus I only did it with single end for now (you could either use R1 or R2).

It would be possible to try it, since Trinity deals with paired-end, however, it would need some changes in the main script and I plan to have a look on it (but I would like to test the impact on the assembly quality before). I keep you in touch !

Does it run well using single end ? I recommend to try different times of Trinity iteration, and choose the number that will ensure the best assembly N50 (on the Trinity.fasta file).



so I thought everything seemed to be running smoothly (as far as I can see) and at the end of the run I got this error.

I dont understand it.

Code:
Loading required package: methods
mv: cannot stat `/lustre/work/daray/software/dnaPipeTE/landscape.pdf': No such file or directory
Done
Finishin time: Wed Apr  8 14:10:52 2015
########################
#   see you soon !!!   #
########################
compute-24-11:/lustre/work/lblancob/TE_annotation2/dnaPipeTE$


Everything seems OK for me. The error you had is related to the graph "landscape.pdf". Do you have it in your outputs ?
If yes, this error is a relicat of old scriptings and do not need attention. If no, there may be an issue with the landscape part.

Sometimes, the landscape graph had some issues: just check that the file "factors and colors" and the file "sorted families" have the same number of lines !


it finally worked, thank you very, very much!
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by eemontiel on Sun Mar 20, 2016 12:20 am

Hi Clement,
I am having troubles with Trinity also. I downloaded the last version of dnaPipeTE (dnaPipeTE_v1.1) and I have followed installation instructions. I am working in a cluster and I think I load all the dependencies required. The thing is that when I run it, I obtain the same error that you mention before:
Code:
awk: cmd. line1: fatal: cannot open file `/work/LAS/emontiel/PEX/output//Trinity_run0/chrysalis/readsToComponents.out.sort' for reading (No such file or directory)
awk: cmd. line1: fatal: cannot open file `/work/LAS/emontiel/PEX/output//Trinity_run1/chrysalis/readsToComponents.out.sort' for reading (No such file or directory)
awk: cmd. line1: fatal: cannot open file `/work/LAS/emontiel/PEX/output//Trinity_run2/Trinity.fasta' for reading (No such file or directory)
RepeatMasker could not find the repeat library at: ./bin/RepeatMasker/Libraries/RepeatMaskerLib.embl
I checked into output folder and those files are not present. Also I was using the specieslib file that you provide and I indicate its position in the arguments when I run it.
Then I took a look of BATCH_OUTPUT file and I found the following line:
Code:
CMD: /data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish count -t 16 -m 25 -s 1 97809618 --both-strands single.fa
/data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish: /lib64/libc.so.6: version 'GLIBC_2.14' not found (required by /data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish)
/data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish: /usr/lib64/libstdc++.so.6: version 'GLINCXX_3.4.15' not found (/data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish
Error, cmd: /data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish count -t 16 -m 25 -s 1497809618 --both-strand single.fa died with ret 256 at //data019/LAS/emontiel/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Trinity.pl line 1597
Any suggestion?
Thank you for your time.
Cheers

eemontiel

Posts : 1
Join date : 2016-03-14

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Sun Mar 20, 2016 1:34 pm

Hi eemontiel!

The first error:
Code:
awk: cmd. line1: fatal: cannot open file `/work/LAS/emontiel/PEX/output//Trinity_run0/chrysalis/readsToComponents.out.sort' for reading (No such file or directory)
is normal, its a small bug I didn't corrected  Very Happy
Then, I think the other two error you have seem to be related to the error you have in the BATCH_OUTPUT; I think some libraries are missing for Jellyfish (Trinity's first step): 'GLIBC_2.14' and 'GLINCXX_3.4.15' from libc and libstdc++.

You can try:

Code:
sudo apt-get update
sudo apt-get install libc6


and

Code:

sudo apt-get install libstdc++6


To update/install these libraries. If everything is correct it should allow Trinity to work! Tell me if it helps!

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by irisxkx on Mon Mar 21, 2016 2:06 pm

Dear Clément,

thanks for the useful forum :-)
I have the same problem mentioned above, with two libraries missing for Jellyfish: 'GLINCXX_3.4.15' and 'GLIBC_2.14'. The problem here is that, according to our awesome HPC support guy: "the first could be solved by loading the module gnu/5.1.0, the second would require a system upgrade, which isn't feasible". Therefore, my question comes down to if you have modified/patched the Trinity script in any way. Our HPC runs a newer version of Trinity (2.0.6), and we could use this version instead, in case it is likely to work with dnaPipeTE.
Looking forward to your suggestions,

Iris

irisxkx

Posts : 4
Join date : 2016-03-21

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Mon Mar 21, 2016 4:50 pm

Hi Iris,

Thanks for your message!
I'm so sorry you also encounter issues with Trinity... Did you try the previous suggestion I made to upgrade the libraries?
I did not modify the Trinity script; however, new versions (>2014-04-13) and so I guess > v.2 has changed the name of the component and thus dnaPipeTE won't be able to parse the files.

Please tell me if you are still stuck with this problem. Can you tell me more about your HPC configuration and system?
Anyway, I should have a look to make dnaPipeTE compatible with the latest version of Trinity, but this will need a bit of development! In between you can try this:

You may solve the problem by re-compiling Trinity according to your local hardware. For that you can download the compatible version of Tritnity for dnaPipeTE here and install it in the ./bin folder of dnaPipeTE instead of the current (and already compiled) one. According to the dnaPipeTE script, the perl script Trinity.pl should be then accessible at ~/yourdirectory/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Trinity.pl

Tell me if it helps!

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by irisxkx on Wed Mar 23, 2016 10:50 am

Hi Clément,

Thanks for your suggestions. It is good to know that I can use an independent installation of Trinity for dnaPipeTE, as long as the version is lower than 2014-04-13. After linking to an earlier Trinity installation, dnaPipeTE runs fine. But I am getting trouble with RepeatMasker; seemingly I am not managing to configure the RepeatMaskerConfig.pm correctly. This is the message:

The RepeatMasker installation directory ($RepeatMaskerConfig::REPEATMASKER_DIR) is incorrectly set in the RepeatMaskerConfig.pm file.  Please open the RepeatMaskerConfig.pm file  and edit the $RepeatMaskerConfig::REPEATMASKER_DIR line.
RepeatMasker version open-4.0.6

I edited the path like this:
$REPEATMASKER_DIR          = "/home/ivargasj/dnaPipeTE/bin/RepeatMasker";

Nevertheless, RepeatMasker still does not pass the initial test. There are many other paths in the RepeatMaskerConfig.pm file that are not set, but I don't think I need them. Do I need to change something else?

Cheers,

Iris

irisxkx

Posts : 4
Join date : 2016-03-21

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Wed Mar 23, 2016 11:24 am

Hi Iris,

That's good that Trinity is now working!
Concerning RepeatMasker, did you run dnaPipeTE from its own folder? You may have a problem of path if you try to run the script from another location, since RM will check if the current path is compatible with its path in the its config file (./bin/RepeatMasker). I have trouble with this self check, and I am working on it to allow running dnaPipeTE from any location. In between, you still have to specify:

Code:
cd ~/yourdirectory/dnaPipeTE/

before launching the script dnaPipeTE.py

So if you did not start dnaPipeTE like this, change back the $REPEATMASKER_DIR to "./bin/RepeatMasker" and run it this way, it should solve the problem. If you have however done this but this wasn't not working, try also to remove the config.ini file before starting dnaPipeTE.

Tell me how it is going on,

Cheers,

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by irisxkx on Wed Mar 23, 2016 11:59 am

Hi Clément,

damn you are fast!
Yep, I run dnaPipeTE.py from inside its directory. I reverted my changes to the RepeatMaskerConfig.pm file and removed the config.ini file. But it still does not work; the newly generated config.ini looks like this:

[DEFAULT]
repeatmasker_library =
trinity_memory = 10G
blast_folder = /home/ivargasj/dnaPipeTE/bin/ncbi-blast-2.2.28+/bin/
parallel = /home/ivargasj/dnaPipeTE/bin/parallel
repeatmasker = /home/ivargasj/dnaPipeTE/bin/RepeatMasker/RepeatMasker
trinity = /home/ivargasj/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Trinity.pl
rm_species = All
sample_number = 2
trf = /home/ivargasj/dnaPipeTE/bin/trf
sample_size = 500000

Any other ideas?

Cheers,
Iris

irisxkx

Posts : 4
Join date : 2016-03-21

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Wed Mar 23, 2016 12:54 pm

Ouch...

I'm sorry, but we will find what's going wrong! Can you send me by MP your whole log/error file(s) for dnaPipeTE?

Cheers,

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Wed Mar 23, 2016 2:51 pm

Thanks for the whole log. Unfortunately, I did not find any cue... :S
However, I am wondering how you did to ask dnaPipeTE to use your own version of Trinity, without making change in the config.ini file? Did you change something in the script itself? Because I see that the path to Trinity used is not the ./bin/Trinity... of dnaPipeTE.
It could help me to see clearer!

Cheers,

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by irisxkx on Wed Mar 23, 2016 4:10 pm

Hmmm, see, I am a biologist, so I basically did not know about the config.ini until you mentioned it :-P And changing a python script Shocked Laughing No no, I did not change nor delete anything, I simply made a symbolic link pointing from the original Trinity directory in dnaPipeTE, 'trinityrnaseq_r2013_08_14', to the Trinity installation with the same version on our server. As far as I can see, Trinity works well, and it also worked nicely when I linked to a new Trinity installation in my home directory (version trinityrnaseq_r20140413p1). I don't see how the Trinity installation should affect RepeatMasker.

To be sure I did not screw anything, I will delete my dnaPipeTE installation, download a fresh copy, decompress it, add the RepBase library and trf, link to our Trinity, and try again...

Cheers,

Iris

irisxkx

Posts : 4
Join date : 2016-03-21

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Wed Mar 23, 2016 4:52 pm

Well, it's not bad at all!

In this way, I'm pretty sure that this would not affect Repeat Masker. I think it is a good idea to restart from scratch. Maybe modifying the RepeatMasker pm file would have screwed something... scratch

Another way to change the path to trinity would be to modify (after a first run that will generate a config.ini file) the path to Trinity in the config.ini file, that wont be replaced after (it is created at the first run according to your install, and then is not produced unless it has been removed). But I think using symbolic link is great too!

Tell me how it goes,

Cheers,

Clément

avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Fri Apr 22, 2016 3:50 pm

Hello,

I have the same problem than above.
Do you know where I can download the trinity r2013_08_14 version ?

Or, do you plan to update your script with the new trinity ??

ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Fri Apr 22, 2016 3:58 pm

Hello ptranvan,

Here is a link to r2013_08_14 ftp://pbil.univ-lyon1.fr/pub/divers/goubert/trinityrnaseq_r20140413p1.tar.gz
This is on my to-do list, but unfortunately, I don't have so much time for that now... Sad
I let you now for the next updates!

Cheers,

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Fri Apr 22, 2016 4:10 pm

Ok, thanks.
I don't have the lib error anymore, but I got another one:


CMD: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Chrysalis//../trinity-plugins/coreutils/bin/sort --parallel=1 -T . -S 10G -k 1,1n /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis/readsToComponents.out > /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis/readsToComponents.out.sort
sh: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Chrysalis//../trinity-plugins/coreutils/bin/sort: Aucun fichier ou dossier de ce type

Seems like readsToComponents.out.sort doesn't exist

ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Fri Apr 22, 2016 4:14 pm

To better understand where the error is, could you send the exact command of your job, and also the log file?

In addition, you can try to remove the config.ini file before a new test.
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Fri Apr 22, 2016 4:20 pm

1)I'm testing your pipeline with the test dataset so the command is :

Code:

python3 ./dnaPipeTE.py -input test_dataset.fastq -output output_folder -genome_size 1000000 -genome_coverage 0.1 -sample_number 1

2) I've ran without the config.ini: same problem.

3) There is no log file but here is the last errors:



-------------------------------------------
---- Chrysalis: ReadsToTranscripts --------
-- (Place reads on Inchworm Bundles) ------
-------------------------------------------

Setting maximum number of reads to load in memory to 1000000
-setting num threads to: 1
Reading bundled inchworm contigs...
done!
Assigning kmers to Iworm bundles ... done!
Processing reads:
reading another 1000000... done
[1204] reads analyzed for mapping.
[1] components written.
reading another 1000000... finished reading reads
Done
CMD: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Chrysalis//../trinity-plugins/coreutils/bin/sort --parallel=1 -T . -S 10G -k 1,1n /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis/readsToComponents.out > /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis/readsToComponents.out.sort
sh: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Chrysalis//../trinity-plugins/coreutils/bin/sort: Aucun fichier ou dossier de ce type
COMMAND: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Chrysalis//../trinity-plugins/coreutils/bin/sort --parallel=1 -T . -S 10G -k 1,1n /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis/readsToComponents.out > /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis/readsToComponents.out.sort
Died with exit code 32512
Exiting.
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 4134528
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 12288
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

Error, the Chrysalis process failed:
Error, cmd: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Chrysalis/Chrysalis -i single.fa -iworm /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/inchworm.K25.L25.DS.fa -o /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_folder/Trinity_run1/chrysalis -cpu 1 -min_glue 1 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 -sort_buffer_size 10G -max_mem_reads 1000000 -butterfly /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Butterfly/Butterfly.jar 2>&1 died with ret 65280 at /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Trinity.pl line 1597.

at /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Trinity.pl line 1191.
main::run_chrysalis('/stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/output_...', 'single.fa', 200, 500, undef, 'single.fa') called at /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/bin/trinityrnaseq_r2013_08_14/Trinity.pl line 1015
Trinity iteration 1 Done'
renaming Trinity output...
awk: cmd. ligne:1: Fatal: ne peut ouvrir le fichier « output_folder/Trinity_run1/Trinity.fasta » en lecture (Aucun fichier ou dossier de ce type)
done
output_folder/Annotation/one_RM_hit_per_Trinity_contigs
output_folder/Annotation/Best_RM_annot_80-80
output_folder/Annotation/Best_RM_annot_partial
#######################################
### REPEATMASKER to anotate contigs ###
#######################################

RepeatMasker version open-4.0.6
Search Engine: NCBI/RMBLAST [ 2.2.27+ ]
Master RepeatMasker Database: ./bin/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20150807 )


File output_folder/Trinity.fasta appears to be empty.
Traceback (most recent call last):
File "./dnaPipeTE.py", line 700, in <module>
RepeatMasker(config['DEFAULT']['RepeatMasker'], args.RepeatMasker_library, args.RM_species, args.cpu, args.output_folder, args.RM_threshold)
File "./dnaPipeTE.py", line 359, in __init__
self.repeatmasker_run()
File "./dnaPipeTE.py", line 378, in repeatmasker_run
with open(self.output_folder+"/Trinity.fasta.out", 'r') as trinity_handle:
FileNotFoundError: [Errno 2] No such file or directory: 'output_folder/Trinity.fasta.out'



ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Fri Apr 22, 2016 5:00 pm

Ok I found a solution for the previous problem bt now I got anoter one ...


#######################################################
### Blast 1 : raw reads against all repeats contigs ###
#######################################################
Blast 1 files found, skipping Blast 1 ...
###################################################
### Blast 2 : raw reads against annoted repeats ###
###################################################
Blast 2 files found, skipping Blast 2 ...
#####################################################
### Blast 3 : raw reads against unannoted repeats ###
#####################################################
blasting...


Building a new DB, current time: 04/22/2016 16:59:55
New DB name: output_folder/blast_out/blast3_db.fasta
New DB title: output_folder/Annotation/unannoted.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: File output_folder/Annotation/unannoted.fasta is empty
Paring blast3 output...
sort: échec d'ouverture: output_folder/blast_out/reads_vs_unannoted.blast.out: Aucun fichier ou dossier de ce type
rm: impossible de supprimer « output_folder/blast_out/int.reads_vs_annoted.blast.out »: Aucun fichier ou dossier de ce type
#######################################################
### Estimation of Repeat content from blast outputs ###
#######################################################
parsing blastout and adding RM annotations for each read...
join: contigsTrinityRM.sorted: Aucun fichier ou dossier de ce type
Done, results in: blast_out/blastout_final_fmtd_annoted
#########################################
### OK, lets build some pretty graphs ###
#########################################
Drawing graphs...
/bin/sh: /stn4/ul/monthly/ptranvan/synergia/software/dnaPipeTE/graph.R : /usr/bin/Rscript : mauvais interpréteur: Aucun fichier ou dossier de ce type
Done
Removing Trinity runs files...
find: "output_folder/Trinity_run*": Aucun fichier ou dossier de ce type
done
Finishin time: Fri Apr 22 14:59:55 2016
########################
# see you soon !!! #
########################


ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Fri Apr 22, 2016 5:03 pm

Ok, can you explain how did you managed to get rid off your first problem?

Try to remove the output folder before doing another test, the last failed run may have messed up the whole thing!
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Fri Apr 22, 2016 5:06 pm

Clément Goubert wrote:Ok, can you explain how did you managed to get rid off your first problem?

Try to remove the output folder before doing another test, the last failed run may have messed up the whole thing!


I've downloaded the trinity you've provided with your link.

SO the version seems different from the original one (20140413 instead of 2013_08_14).

Then I modified the trinity environment in the config gile:

trinity = bin/trinityrnaseq_r20140413p1/Trinity

ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Mon Apr 25, 2016 2:26 pm

Ok!

Sorry for my late response. Did you re-run dnaPipeTE after removal of your old output folder? Have you still the same issue?

Thanks!

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Mon Apr 25, 2016 4:41 pm

No, I don't know how to manage it Sad

Blast 3 seems not to work ...


ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Tue Apr 26, 2016 4:28 pm

ptranvan wrote:No, I don't know how to manage it Sad


What do you mean exactly? cyclops
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by ptranvan on Wed Apr 27, 2016 10:49 am

Clément Goubert wrote:
ptranvan wrote:No, I don't know how to manage it Sad


What do you mean exactly? cyclops

I mean, I have the same error:


#####################################################
### Blast 3 : raw reads against unannoted repeats ###
#####################################################
blasting...


Building a new DB, current time: 04/26/2016 19:20:45
New DB name:   outp/blast_out/blast3_db.fasta
New DB title:  outp/Annotation/unannoted.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: File outp/Annotation/unannoted.fasta is empty
Paring blast3 output...
sort: échec d'ouverture: outp/blast_out/reads_vs_unannoted.blast.out: Aucun fichier ou dossier de ce type
rm: impossible de supprimer « outp/blast_out/int.reads_vs_annoted.blast.out »: Aucun fichier ou dossier de ce type
#######################################################
### Estimation of Repeat content from blast outputs ###
#######################################################
parsing blastout and adding RM annotations for each read...
join: contigsTrinityRM.sorted: Aucun fichier ou dossier de ce type
Done, results in: blast_out/blastout_final_fmtd_annoted
#########################################
### OK, lets build some pretty graphs ###
#########################################
Drawing graphs...
/bin/sh: /stn4/ul/monthly/ptranvan/Software/dnaPipeTE/1.2/graph.R : /usr/bin/Rscript : mauvais interpréteur: Aucun fichier ou dossier de ce type
Done
Removing Trinity runs files...
find: "outp/Trinity_run*": Aucun fichier ou dossier de ce type
done
Finishin time: Tue Apr 26 17:20:49 2016
########################
#   see you soon !!!   #
########################

by using your test dataset and your command, as described here (github.com/clemgoub/dnaPipeTE):

python3 ./dnaPipeTE.py -input ./test/test_dataset.fastq -output ~/path/to/the/output_folder -genome_size 1000000 -genome_coverage 0.1 -sample_number 1

ptranvan

Posts : 13
Join date : 2016-04-22

View user profile

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Clément Goubert on Wed Apr 27, 2016 1:33 pm

Hello,

I think the problem is my fault, I put a too small number of reads to be sampled in the command of the test run, try with:

python3 ./dnaPipeTE.py -input test_dataset.fastq -output ~/path/to/the/output_folder -genome_size 10000000 -genome_coverage 0.1 -sample_number 1

(10,000,000 instead of 1,000,000 bp for genome size will give more reads to process).

In addition, I fixed a small bug in the dnaPipeTE.py script that avoid the error:
Code:
rm: impossible de supprimer « outp/blast_out/int.reads_vs_annoted.blast.out »: Aucun fichier ou dossier de ce type

Tell me if it fixed it!

Clément
avatar
Clément Goubert
Admin

Posts : 30
Join date : 2016-01-05
Age : 29

View user profile https://lbbe.univ-lyon1.fr/-dnaPipeTE-.html

Back to top Go down

Re: Installation issues starting with Trinity [SOLVED]

Post by Sponsored content


Sponsored content


Back to top Go down

Page 1 of 2 1, 2  Next

View previous topic View next topic Back to top

- Similar topics

 
Permissions in this forum:
You cannot reply to topics in this forum