Open oushujun opened 4 years ago
I misread what your issue was before - in multiple ways. Sorry about that...
I believe this is actually a bug. It looks like RepeatModeler
does not pass command-line path overrides down to LTRPipeline
.
As a workaround, an environment variable ought to work properly: NINJA_DIR=/home/oushujun/las/bin/NINJA/NINJA /usr/bin/time -v RepeatModeler -engine ncbi -pa $threads -database $genome -LTRStruct -debug
Seems like this is an independent issue so I open this new thread.
Since the conda RepeatMasker
error I encountered and described above, I installed the full version (v2.0.1) of RepeatMasker
with the configure
script. I re-executed the full pipeline and still encounter the same Ninja error:
Clustering...LTRPipeline::runNinja : tmpdir = .../RepeatModeler/RM_163533.MonM ar301322402020/LTR_53177.TueMar311844022020/NINJA_53177.TueMar311953202020 LTRPipeline::runNinja : Running analysis /home/oushujun/las/bin/NINJA/NINJA//Ninja --in .../RepeatModeler/RM_163533.MonMar301322402020/LTR_53177.TueMar311844022020/mafft-alignment.fa --out .../RepeatModeler/RM_163533.MonMar301322402020/LTR_53177.TueMar311844022020/NINJA_53177.TueMar311953202020/cl uster.dat --out_type c --corr_type m --cluster_cutoff 0.2 --threads 36 > .../R epeatModeler/RM_163533.MonMar301322402020/LTR_53177.TueMar311844022020/NINJA_53177.TueMar311953202020/Ninja.log 2>&1 LTRPipeline: Error - could not cluster MAFFT results. : 00:00:00 (hh:mm:ss) Elapsed Time
Except for this time the Ninja error log shows:
sh: /home/oushujun/las/bin/NINJA/NINJA//Ninja: cannot execute binary file
There is a double "/" in the command but I assume this would not affect the execution of this program. Then I check the precompiled Ninja program, it could not be executed in my Linux system...
So I think you are right, the -ninja_dir
parameter is not passed down to the LTRPipeline
.
Then I check the precompiled Ninja program, it could not be executed in my Linux system...
Where did you get a precompiled Ninja program? Those might have been accidentally committed to the repository at one point but I thought those had been cleaned up by now.
It was from the NINJA repository, but I think I didn't use the NINJA 0.95-cluster_only
version. I will try that.
There are executables called Ninja_new
and Ninja_old
in the NINJA 0.95-cluster_only
package, both reported errors like these:
./Ninja_new: /lib64/libstdc++.so.6: version
GLIBCXX_3.4.20' not found (required by ./Ninja_new) ./Ninja_new: /lib64/libstdc++.so.6: version
CXXABI_1.3.8' not found (required by ./Ninja_new) ./Ninja_new: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./Ninja_new)
I could recompile it with make all
but only got a program named Ninja
, which seems executable. Should I use this for RepeatModeler
?
Yes - Ninja
built by make
is the correct one. Sorry about that, I really thought those were cleaned up but there are more leftover binaries in there than I realized.
I had this same issue. A more permanent workaround for me was creating a symlink to Ninja in the directory where the pipeline expected it.
I got the same issue.
It seems that ninjia did not produce a clusters.dat file as RepeatModeler expected, but ninjia did produce something: -rw-rw-r-- 1 lcz lcz 6612177 Aug 14 17:23 LtrRetriever-redundant-results.fa -rw-rw-r-- 1 lcz lcz 275719074 Aug 14 18:17 mafft-alignment.fa -rw-rw-r-- 1 lcz lcz 2847322 Aug 14 16:22 raw-struct-results.txt
So I guess it is something about the version of ninjia? The ninjia I used was the precompiled NINJA-0.95-cluster_only/Ninja_new which I made a soft link as Ninjia.
@lczqd those are not outputs of ninja. raw-struct-results.txt
is a product of LTRHarvest, LtrRetriever-redundant-results.fa
of LTR_Retriever and mafft-alignment.fa
a product of MAFFT. What does your log say?
Im having the same issue, the pipeline is failing in
lustering...LTRPipeline::runNinja : tmpdir = /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/NINJA_1415401.FriAug200354262021 LTRPipeline::runNinja : Running analysis /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/repeatmodeler/bin/Ninja --in /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/mafft-alignment.fa --out /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/NINJA_1415401.FriAug200354262021/cluster.dat --out_type c --corr_type m --cluster_cutoff 0.2 --threads 70 > /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/NINJA_1415401.FriAug200354262021/Ninja.log 2>&1 LTRPipeline: Error - could not cluster MAFFT results. : 00:00:00 (hh:mm:ss) Elapsed Time LTRPipeline : Error - could not open /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/clusters.dat! at /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/repeatmodeler/share/RepeatModeler/LTRPipeline line 325.
Any ideas? The Ninja file seems to be working ok.
The ninjia I used was the precompiled NINJA-0.95-cluster_only/Ninja_new which I made a soft link as Ninjia.
@lczqd Please see the previous comments about this exact problem: https://github.com/Dfam-consortium/RepeatModeler/issues/74#issuecomment-608022714. The precompiled programs have never been updated and were only included by accident; in the latest release https://github.com/TravisWheelerLab/NINJA/releases/tag/0.98-cluster_only these have been removed to avoid the confusion in the future.
The ninjia I used was the precompiled NINJA-0.95-cluster_only/Ninja_new which I made a soft link as Ninjia.
@lczqd Please see the previous comments about this exact problem: #74 (comment). The precompiled programs have never been updated and were only included by accident; in the latest release https://github.com/TravisWheelerLab/NINJA/releases/tag/0.98-cluster_only these have been removed to avoid the confusion in the future.
Thanks. That was what I did. I compiled ninja from source code and the problem was solved.
clusters.dat Im having the same issue, the pipeline is failing in
lustering...LTRPipeline::runNinja : tmpdir = /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/NINJA_1415401.FriAug200354262021 LTRPipeline::runNinja : Running analysis /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/repeatmodeler/bin/Ninja --in /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/mafft-alignment.fa --out /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/NINJA_1415401.FriAug200354262021/cluster.dat --out_type c --corr_type m --cluster_cutoff 0.2 --threads 70 > /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/NINJA_1415401.FriAug200354262021/Ninja.log 2>&1 LTRPipeline: Error - could not cluster MAFFT results. : 00:00:00 (hh:mm:ss) Elapsed Time LTRPipeline : Error - could not open /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/eutypa_lata/repeatmodeler/RM_1378244.ThuAug191026162021/LTR_1415401.FriAug200351142021/clusters.dat! at /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/repeatmodeler/share/RepeatModeler/LTRPipeline line 325.
Any ideas? The Ninja file seems to be working ok.
Compile ninja from source code will solve the problem. The pre-compiled ninja is outdated.
Hello,
I am facing the same issue. I compiled Ninja from the source and still I am having a segmentation fault issue.
NINJA-0.95-cluster_only/NINJA/Ninja --in mafft-alignment.fa --out cluster.dat --out_type c --corr_type m --cluster_cutoff 0.2 --cluster_cutoff 0.2
Reading...
Segmentation fault
Any ideas how to solve this issue? Best, André
@deoliveira86 Could you share the failing mafft-alignment.fa file that is causing this failure?
@jebrosen So I rerun the conda
RepeatModeler
with-debug
with the following command:I received these errors in the LTRStruc step:
I checked the log file
NINJA_<num>.<date>/Ninja.log
and it has the following error msg:It seems that
RepeatModeler
is not picking up the provided NINJA path, can you help to check?Shujun
Originally posted by @oushujun in https://github.com/Dfam-consortium/RepeatModeler/issues/62#issuecomment-606153508