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View Code? Open in Web Editor NEWA tool for discovering transposable elements and describing patterns of genome evolution
License: MIT License
A tool for discovering transposable elements and describing patterns of genome evolution
License: MIT License
This results from transforming the IDs to write the GFF with unique IDs; the simple fix is to write a new sequence record with the same ID.
I fixed the issue of the missing TephraDB files by copying them manually and changing the configuration (Apparently singularity wants the user to be root, but that needs the --fakeroot command to work, which is difficult) -- I think you could rebuild it to work around that at some point.
But now I am receiving an illegal option -j
`INFO - ======== Tephra version: 0.12.5 (started at: 10-06-2020 05:41:14) ========
INFO - Configuration - Log file for monitoring progress and errors: tephra_full.log
INFO - Configuration - Genome file: polished_1.fasta.masked
INFO - Configuration - Repeat database: consensi.fa.classified
INFO - Configuration - Number of threads: 24
INFO - Command - 'tephra findltrs' started at: 10-06-2020 05:41:14.
sh: 0: Illegal option -j
ERROR - 'gt suffixerator' failed with exit value: 2. Here is the output:
INFO - Command - 'tephra findltrs' completed at: 10-06-2020 05:41:15.
INFO - Command - 'tephra findtrims' started at: 10-06-2020 05:41:15.
[ERROR]: Copy failed: No such file or directory
INFO - Command - 'tephra findtrims' completed at: 10-06-2020 05:41:16.
INFO - Command - 'tephra findhelitrons' started at: 10-06-2020 05:41:16.
[ERROR]: Could not open file: /db/polished_1_tephra_hscan_helitrons.hel.fa
INFO - Command - 'tephra findhelitrons' completed at: 10-06-2020 05:41:38.
INFO - Command - 'tephra findtirs' started at: 10-06-2020 05:41:38.
Copy failed: No such file or directory at /usr/local/share/perl/5.26.1/Tephra/Command/findtirs.pm line 73.
INFO - Command - 'tephra findtirs' completed at: 10-06-2020 05:41:39.
Use of uninitialized value $tirc_fas in -e at /usr/local/share/perl/5.26.1/Tephra/Command/all.pm line 282.
INFO - Command - 'tephra findnonltrs' started at: 10-06-2020 05:41:39.
`
Any ideas?
The identifiers from the classifyltrs
subcommand are different from the ltrage
command. This is not a bug per se, but it should be standardized to make it easier to understand the results.
Installed everything as required (and a few more perl libs) and now I get the following. Seems like a problem with Bio/DB/HTS specifically, I installed htslib as required and the module manually.
tephra all -c tephra_config.yml
Can't load '/usr/local/lib/x86_64-linux-gnu/perl/5.22.1/auto/Bio/DB/HTS/HTS.so' for module Bio::DB::HTS: libhts.so.2: cannot open shared object file: No such file or directory at /usr/lib/x86_64-linux-gnu/perl/5.22/DynaLoader.pm line 187.
at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71.
BEGIN failed--compilation aborted at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/share/perl/5.22.1/Tephra/Stats/Age.pm line 17.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.22.1/Tephra/Stats/Age.pm line 17.
Compilation failed in require at /usr/local/share/perl/5.22.1/Tephra/Command/age.pm line 11.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.22.1/Tephra/Command/age.pm line 11.
Compilation failed in require at /usr/local/share/perl/5.22.1/App/Cmd.pm line 194.
App::Cmd::_command("Tephra", HASH(0x1374f30)) called at /usr/local/share/perl/5.22.1/App/Cmd.pm line 171
App::Cmd::new("Tephra", HASH(0x1374f30)) called at /usr/local/bin/tephra
The CLI arguments should override the configuration, and the behavior should be known and documented.
These are problematic on RHEL-based systems like CentOS because they are missing from the package managers. It is not ideal to have a completely different different set of install instructions for different Linux OSs because this makes testing nearly impossible.
Hi, I have a bug report and an issue.
My data consisted of nine long contigs and many short contigs.
At first, I analyzed the whole data, but it didn't work, so I tried to analyze 9 long contigs one by one.
As results, although I saw [ERROR] as shown below in all of 9 data, Tephra completed analysis for 4 contigs.
But the analysis stopped at the 'tephra findtirs' for the remaining five long contigs.
I would appreciate any advice on those issues.
Below are messages of bug report (ERROR), and the last lines of the error log when the analysis stopped.
#macOS 10.15.7
#Docker Desktop 3.6.0 (3.6.0.5487)
#Tephra version: 0.13.2
[ERROR]: LTR_retrotransposon1190_SCAffold not found in store of Tephra::Classify::Fams::make_fasta_from_dom_orgs. This is a bug, please report it.
[ERROR]: (LARD_retrotransposon1_SCAffold_4862_49847_50712) not found in family/singleton name map. This is a bug, please report it. Exiting.
INFO - Command - 'tephra findtirs' started at: 02-01-2022 10:02:26.
[fai_load] build FASTA index.
Can't use an undefined value as an ARRAY reference at /usr/local/share/perl/5.30.0/Tephra/Role/GFF.pm line 235.
Unable to run 'tephra findtirs'. Here is the exception: "tephra" unexpectedly returned exit value 38 at /usr/local/share/perl/5.30.0/Tephra/Role/Run/TephraCmd.pm line 46.
Thanks
Dear Evan,
I am really excited with getting Tephra running, it seems to be a beautiful piece of software. I had some issues I'd like to solve, though. I am putting them here so everyone can see, but please let me know if this shouldn't be on the issues.
I got the docker version running by installing docker:
$ docker run -it --name tephra-con -v $(pwd)/db:/db:Z sestaton/tephra
$ cd /db
$ wget https://raw.githubusercontent.com/sestaton/tephra/master/config/tephra_config.yml
#### changed the "logfile", "genome", "outfile", "repeatdb" (using your sunflower library, thank you for that!).
$ tephra all -c tephra_config.yml
[ERROR]: gene file was not defined in configuration or does not exist. Check input. Exiting.
I noticed that the new config file has this line. It is possibly new since it is not on the manual or help pages.
I deleted it:
$ sed "s/.*genefile.*//; /^$/d" tephra_config.yml > tephra_config2.yml
$ tephra all -c tephra_config2.yml
[ERROR]: 'trnadb' under 'all' is not defined after parsing configuration file.
This indicates there may be a blank line in your configuration file.
Please check your configuration file and try again. Exiting.
Q1: I interpret this that it did not like my re-formating of the config file. I was thus wondering what is this "TAIR10_genes.fas". Is this the genetic annotations of arabidopsis? I checked NCBI and TAIR10 seems to be an assembly name for this species ( https://www.ncbi.nlm.nih.gov/assembly/GCF_000001735.4).
Q2: Is there a way to run the "all" command without specifying the annotations?
See config file below.
$ cat t*yml
## For more information about this file, see:
## https://github.com/sestaton/tephra/wiki/Specifications-and-example-usage.
all:
- logfile: tephra.log
- genome: scalesia_atractyloides.fasta
- outfile: scalesia_atractyloides_thra_transposons.gff3
- repeatdb: Ha412v1r1_transposons_v1.0.fasta
- genefile: TAIR10_genes.fas
- trnadb: TephraDB
- hmmdb: TephraDB
- threads: 24
- clean: YES
- debug: NO
- subs_rate: 1e-8
findltrs:
- dedup: NO
- tnpfilter: NO
- domains_required: NO
- ltrharvest:
- mintsd: 4
- maxtsd: 20
- minlenltr: 100
- maxlenltr: 1000
- mindistltr: 1000
- maxdistltr: 15000
- seedlength: 30
- tsdradius: 60
- xdrop: 5
- swmat: 2
- swmis: -2
- swins: -3
- swdel: -3
- overlaps: best
- ltrdigest:
- pptradius: 30
- pptlen: 8 30
- pptagpr: 0.25
- uboxlen: 3 30
- uboxutpr: 0.91
- pbsradius: 30
- pbslen: 11 30
- pbsoffset: 0 5
- pbstrnaoffset: 0 5
- pbsmaxeditdist: 1
- pdomevalue: 1E-6
- pdomcutoff: NONE
- maxgaplen: 50
classifyltrs:
- percentcov: 50
- percentid: 80
- hitlen: 80
illrecomb:
- repeat_pid: 10
ltrage:
- all: NO
maskref:
- percentid: 80
- hitlength: 70
- splitsize: 5000000
- overlap: 100
sololtr:
- percentid: 39
- percentcov: 80
- matchlen: 80
- numfamilies: 20
- allfamilies: NO
tirage:
- all: NO
Hello,
I don't have sudo
privileges on our HPC platform, so I could not use the docker
nor the regular installation method. Instead, I am trying to install tephra
via singularity
.
System confirguations:
Red Hat Enterprise Linux Server 7.6 (Maipo)
Perl version v5.24.1
Singularity version v3.1.1
So I can install tephra
using the following command without error:
singularity run docker://sestaton/tephra
Then I type tephra
and it shows help info with some warnings for perl:
$tephra
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Tephra version 0.12.4
Copyright (C) 2015-2019 S. Evan Staton
LICENSE -- MIT
...
I download the tephra_config.yml
file and modified the genome name, then run:
tephra all -c tephra_config.yml
I got the following error messages:
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Can't load '/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/auto/Bio/DB/HTS/HTS.so' for module Bio::DB::HTS: libhts.so.1: cannot open shared object file: No such file or directory at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187.
at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Kseq.pm line 71.
BEGIN failed--compilation aborted at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/share/perl/5.26.1/Tephra/Stats/Age.pm line 17.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.26.1/Tephra/Stats/Age.pm line 17.
Compilation failed in require at /usr/local/share/perl/5.26.1/Tephra/Command/age.pm line 11.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.26.1/Tephra/Command/age.pm line 11.
Compilation failed in require at /usr/local/share/perl/5.26.1/App/Cmd.pm line 194.
App::Cmd::_command("Tephra", HASH(0x55dfea2ba1e0)) called at /usr/local/share/perl/5.26.1/App/Cmd.pm line 171
App::Cmd::new("Tephra", HASH(0x55dfea2ba1e0)) called at /usr/local/bin/tephra line 25
Is it something wrong with my perl version? Or is it approachable to install it via singularity
?
Thanks,
Shujun
[ERROR]: LTR_retrotransposon1587_scaffold not found in store of Tephra::Classify::Fams::make_fasta_from_dom_orgs. This is a bug, please report it.
Dear, I want to use tephra, however, when I installed it, there are some error message as followings. Could you help me to address them?
[root@fat01 tephra]# export TEPHRA_DIR=/opt/software/tephra_fat/tephra
[root@fat01 tephra]# perl Makefile.PL
Warning: prerequisite App::Cmd 0 not found.
Warning: prerequisite List::UtilsBy 0 not found.
Warning: prerequisite Number::Range 0 not found.
Warning: prerequisite Parallel::ForkManager 0 not found.
Warning: prerequisite Set::IntervalTree 0 not found.
Warning: prerequisite Sort::Naturally 0 not found.
Warning: prerequisite Statistics::Descriptive 0 not found.
Warning: prerequisite autodie 0 not found.
Generating a Unix-style Makefile
Writing Makefile for Tephra
Writing MYMETA.yml and MYMETA.json
=====> Configuring Tephra, this may take some time......stopwatch.c: In function ‘format_time_string’:
stopwatch.c:84:3: internal compiler error: Illegal instruction
h = (int) (sec / 3600.);
^
vectorops.c: In function ‘DLog’:
vectorops.c:242:5: internal compiler error: Illegal instruction
else vec[x] = -DBL_MAX;
^~~~
alistat_main.c: In function ‘main’:
alistat_main.c:222:10: internal compiler error: Illegal instruction
best * 100., msa->sqname[bestj],
^~~~
0x9d429f crash_signal
../.././gcc/toplev.c:337
0x9d429f crash_signal
../.././gcc/toplev.c:337
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please submit a full bug report,
with preprocessed source if appropriate.
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
Please include the complete backtrace with any bug report.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
See https://gcc.gnu.org/bugs/ for instructions.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [stopwatch.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [vectorops.o] Error 1
make[1]: *** [alistat_main.o] Error 1
stopwatch.c: In function ‘format_time_string’:
stopwatch.c:84:3: internal compiler error: Illegal instruction
h = (int) (sec / 3600.);
^
vectorops.c: In function ‘DLog’:
vectorops.c:242:5: internal compiler error: Illegal instruction
else vec[x] = -DBL_MAX;
^~~~
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [stopwatch.o] Error 1
make[1]: *** Waiting for unfinished jobs....
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [vectorops.o] Error 1
core_algorithms.c: In function ‘P7ViterbiTrace’:
core_algorithms.c:729:4: internal compiler error: Illegal instruction
if (Prob2Score(hmm->begin[k+1], hmm->p1) + 1 * INTSCALE <= hmm->bsc[k+1])
^~
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [core_algorithms.o] Error 1
make[1]: *** Waiting for unfinished jobs....
display.c: In function ‘PrintIscore’:
display.c:335:3: internal compiler error: Illegal instruction
div = INTSCALE / 0.693147180559945; /* == INTSCALE / log(2) */
^~~
emulation.c: In function ‘WriteProfile’:
emulation.c:179:4: internal compiler error: Illegal instruction
sc = sc * 100 / INTSCALE;
^~
core_algorithms.c: In function ‘P7ViterbiTrace’:
core_algorithms.c:729:4: internal compiler error: Illegal instruction
if (Prob2Score(hmm->begin[k+1], hmm->p1) + 1 * INTSCALE <= hmm->bsc[k+1])
^~
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [display.o] Error 1
make[1]: *** Waiting for unfinished jobs....
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [emulation.o] Error 1
make[1]: *** [core_algorithms.o] Error 1
evd_test.c: In function ‘main’:
evd_test.c:109:3: internal compiler error: Illegal instruction
mu = -20.0;
^~
0x9d429f crash_signal
../.././gcc/toplev.c:337
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://gcc.gnu.org/bugs/ for instructions.
make[1]: *** [evd_test.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2
make failed: Inappropriate ioctl for device at lib/Tephra/Config/Install.pm line 319.
Use example from Arabidopsis or Drosophila because they go quite fast.
This needs to be redesigned but for now a fix is to just use 1 thread.
Also, baseml parser needs to be reconfigured because it is not working on all inputs.
For some domains, such as the LTRs, the feature clustering for family classification is taking way too long to be practical. Need to consider alternatives or optimize the conditions with Vmatch.
Hi Evan,
Thanks for this tool. I wanted to report an error running the tephra age command to estimate tir age. I'm running this in a docker container. Here is the error:
Can't use an undefined value as an ARRAY reference at /usr/local/share/perl/5.26.1/Tephra/Role/GFF.pm line 234
Here is the command that I issued:
tephra age -f r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs_classified.gff3 -g r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe.fasta -o tir_age.txt -i /db --type tir --all
Here are the contents of my db directory:
-rw-rw-r--. 1 1004 1004 897M May 29 15:54 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe.fasta
-rw-rw-r--. 1 1004 1004 15M May 29 15:54 Repeats_noUnkown.lib
-rw-rw-r--. 1 1004 1004 1.8K May 29 15:55 tephra_config.yml
-rw-r--r--. 1 root root 347K Jun 1 13:30 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe.fasta.fai
-rw-r--r--. 1 root root 665K Jun 2 07:16 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked.fasta.log
-rw-r--r--. 1 root root 897M Jun 2 07:16 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked.fasta
-rw-r--r--. 1 root root 347K Jun 2 16:03 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked.fasta.fai
-rw-r--r--. 1 root root 22K Jun 2 16:24 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_gypsy_domain_org.tsv
-rw-r--r--. 1 root root 41K Jun 2 16:24 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_copia_domain_org.tsv
-rw-r--r--. 1 root root 13K Jun 2 16:24 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_unclassified_domain_org.tsv
-rw-r--r--. 1 root root 3.6M Jun 2 18:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified_family-level_domain_org.tsv
-rw-r--r--. 1 root root 85M Jun 2 18:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified.fasta
-rw-r--r--. 1 root root 45M Jun 2 18:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified.gff3
-rw-------. 1 root root 13M Jun 4 17:47 tephra_transposons_hmmdb_tFoH.hmm
-rw-------. 1 root root 0 Jun 4 17:47 tephra_suffixerator_errors_Iee6.err
drwxr-x--x. 1 root root 72 Jun 4 17:58 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims_classified_ltrages/
-rw-r--r--. 1 root root 41M Jun 7 13:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs.gff3
-rw-r--r--. 1 root root 587M Jun 7 13:42 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs.fasta
-rw-r--r--. 1 root root 4.0M Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_trims.gff3
-rw-------. 1 root root 4.1M Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_trims.fasta
-rw-r--r--. 1 root root 45M Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_trims.fasta
-rw-r--r--. 1 root root 8.2K Jun 7 22:11 elata_r4_full.log
-rw-r--r--. 1 root root 0 Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked2.fasta
drwxr-x--x. 1 root root 331K Jun 7 22:11 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked_tephra_masked_tmp/
-rw-r--r--. 1 root root 67K Jun 7 22:37 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_masked2.fasta.log
-rw-r--r--. 1 root root 22K Jun 7 23:07 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_gypsy_domain_org.tsv
-rw-r--r--. 1 root root 41K Jun 7 23:07 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_copia_domain_org.tsv
-rw-r--r--. 1 root root 13K Jun 7 23:07 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_unclassified_domain_org.tsv
drwxr-x--x. 1 root root 452 Jun 7 23:07 ltrs_classified/
-rw-r--r--. 1 root root 3.6M Jun 8 00:14 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_classified_family-level_domain_org.tsv
-rw-r--r--. 1 root root 2.3K Jun 8 00:15 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_classifyltrs.log
-rw-r--r--. 1 root root 295M Jun 8 00:15 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_classified.fasta
-rw-r--r--. 1 root root 42M Jun 8 00:15 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_ltrs_classified.gff3
-rw-r--r--. 1 root root 3.8M Jun 8 01:11 ltr_age.txt
-rw-r--r--. 1 root root 20M Jun 8 19:05 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs.gff3
-rw-r--r--. 1 root root 87M Jun 8 19:05 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs.fasta
-rw-r--r--. 1 root root 3.0K Jun 8 20:28 r4_Oen_Jan2017PB_scaff.final.scaffolds.nopipe_tephra_tirs_tc1-mariner_domain_org.tsv
Notably, I didn't encounter this issue when I ran the tephra age command on ltrs. Any idea what could be happening?
Thanks!
Dave
The feature coordinates seem to have been messed up slightly in the refinements step with the LTR element having coordinates outside the parent repeat_region.
The environment is still hard coded in one of the classes (RunHMM)..fix it!
Dear:
working with Mac operating system,
**echo "n" | cpanm -n Data::Stag DB_File Bio::Root::Version Bio::SearchIO::blastxml Bio::SearchIO::hmmer**
Data::Stag is up to date. (0.14)
DB_File is up to date. (1.852)
Bio::Root::Version is up to date. (1.7.5)
Bio::SearchIO::blastxml is up to date. (1.70)
Bio::SearchIO::hmmer is up to date. (1.7.3)
**cpanm --installdeps .**
--> Working on .
Configuring /Users/ohon_ad/Downloads/tephra-0.12.3 ... OK
<== Installed dependencies for .. Finishing.
**perl Makefile.PL**
Generating a Unix-style Makefile
Writing Makefile for Tephra
Writing MYMETA.yml and MYMETA.json
=====> Configuring Tephra, this may take some time...rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
.util_lib.c:4:10: fatal error: 'malloc.h' file not found
#include <malloc.h>
^~~~~~~~~~
1 error generated.
make: *** [util_lib.o] Error 1
make failed: No such file or directory at lib/Tephra/Config/Install.pm line 726.
Not sure if this is intended or not, but using the -m flag fails as a result of perl-doc not being installed inside the container.
Steps to reproduce...
singularity pull library://sestaton/default/tephra
singularity exec tephra_latest.sif tephra all -m
ERROR: Could not open file: /home/altingia/software/tephra-0.09.6/t/test_data/ref_tephra_masked4_nonLTRs/b/out2/full at /home/altingia/anaconda2/lib/perl5/site_perl/5.22.0/Tephra/NonLTR/Postprocess.pm line 69.
Hello,
I am trying to run Tephra for the first time using your Docker container. I ran silent run using nohup
in expectation to produce gff file for my assembly
nohup tephra all -c tephra_config.yml
And got following files as output
-rw-r--r-- 1 root root 1462272 Oct 22 20:42 QMD-87_01.1.fasta.index.des
-rw-r--r-- 1 root root 708608 Oct 22 20:42 QMD-87_01.1.fasta.index.md5
-rw-r--r-- 1 root root 167936 Oct 22 20:42 QMD-87_01.1.fasta.index.sds
-rw------- 1 root root 966 Oct 22 20:42 nohup.out
-rw-rw-r-- 1 4886 4886 1764 Oct 20 17:47 tephra_config.yml
-rw------- 1 root root 0 Oct 22 20:42 tephra_suffixerator_errors_oBaE.err
-rw-r--r-- 1 root root 449 Oct 22 20:42 tephra_tair10_full.log
-rw------- 1 root root 12940960 Oct 22 20:42 tephra_transposons_hmmdb_C7Xw.hmm
NO errors in error file,no ssues in log file but the program crashes soon after initiated and nohup.out file contains following message.
"/root/.tephra/gt/bin/gt -j 24 suffixerator -db QMD-87_01.1.fasta -indexname /workdir/TEPHRA/db/QMD-87_01.1.fasta.index -tis -suf -lcp -ssp -sds -des -dna 2> /workdir/TEPHRA/db/tephra_suffixerator_errors_oBaE.err" died to signal "INT" (2) at /usr/local/share/perl/5.26.1/Tephra/Role/Run/GT.pm line 98.
Unable to run 'tephra findltrs'. Here is the exception: "tephra" unexpectedly returned exit value 25 at /usr/local/share/perl/5.26.1/Tephra/Role/Run/TephraCmd.pm line 30.
Not quite sure what is going on. Could you please provide some suggestions of might be happening?
Thanks,
Martina
When i run the tephra to indentify the TE on a new genome, and i had faild with the following problems:
Use of uninitialized value $chromosome in concatenation (.) or string at lib/site_perl/5.14.0/Tephra/Role/Util.pm line 41.
Use of uninitialized value $start in concatenation (.) or string at lib/site_perl/5.14.0/Tephra/Role/Util.pm line 41.
Use of uninitialized value $end in concatenation (.) or string at lib/site_perl/5.14.0/Tephra/Role/Util.pm line 41.
[ERROR]: Something went wrong fetching sequence for ':-'. Got zero length.
at lib/site_perl/5.14.0/Tephra/Genome/Unmask.pm line 78.
The current approach is to only calculate the age of exemplars for efficiency, but it should be clear how to calculate the age of all elements if that is needed.
We have a .fasta file containing LTRs and would like to run the age command on that file, but I cannot see in the docs how to do so.
thanks!
This will improve the quality of annotations for draft genomes. Implemented for the findltrs
command but it is not currently an option.
Would be good to add this to other commands, as ell.
The current approach might create too many open files for draft genomes. Need to refactor so we process contigs in chunks rather than leaving all the intermediate files on disk until after the GFF3 is produced.
Currently, Bio::Tools::GFF is used for parsing GFF3 files, but this module appears to be very slow. Need to test Bio::GFF::LowLevel or implement my own parser.
Now that these routines are stable we should consider performance.
Administrators may want to configure the package in a custom location instead of a user directory.
Need to show how to use local::lib or perlbrew install to quickly set up tephra.
Hello,
I run tephra all and obtain an error at the findtirs step:
INFO - Command - 'tephra findtirs' started at: 10-08-2019 04:52:59.
ERROR - 'gt tirvish' failed exit value: 1. Here is the output: warning: terminal_inverted_repeat_element (generated, line 0) is too short to be translated (0 nt), skipped domain search
When running findtirs alone:
'gt tirvish' failed exit value: 1. Here is the output: warning: terminal_inverte
d_repeat_element (generated, line 0) is too short to be translated (0 nt), skipp
ed domain search
/root/.tephra/gt/bin/gt tirvish: error: query seqid 'chrlg1' could match more th
an one sequence description
The other steps look fine based on the output files. This is the log:
root@bp:~/tephra/db# grep "Output\|Command" tephra_full.log
Command - 'tephra findltrs' started at: 06-08-2019 12:38:21.
Command - 'tephra findltrs' started at: 06-08-2019 12:38:39.
Command - 'tephra findltrs' completed at: 08-08-2019 14:42:41.
Output files - /db/genome_v2_tephra_ltrs.gff3
Output files - /db/genome_v2_tephra_ltrs.fasta
Command - 'tephra maskref' for LTRs started at: 08-08-2019 14:42:41.
Command - 'tephra maskref' completed at: 08-08-2019 18:27:24. Final output file:
Output files - /db/genome_v2_tephra_masked.fasta
Command - 'tephra findtrims' started at: 08-08-2019 18:27:24.
Command - 'tephra findtrims' completed at: 09-08-2019 16:39:19.
Command - 'tephra classifyltrs' started at: 09-08-2019 16:39:24.
Command - 'tephra classifyltrs' completed at: 09-08-2019 18:19:09.
Output files - /db/genome_v2_tephra_ltrs_trims_classified.gff3
Output files - /db/genome_v2_tephra_ltrs_trims_classified.fasta
Command - 'tephra age' started at: 09-08-2019 18:19:09.
Command - 'tephra age' completed at: 09-08-2019 18:20:09.
Output files - /db/genome_v2_tephra_ltrages.tsv
Command - 'tephra maskref' for classified LTRs/TRIMs started at: 09-08-2019 18:20:09.
Command - 'tephra maskref' completed at: 09-08-2019 20:22:53. Final output file:
Output files - /db/genome_v2_tephra_masked2.fasta
Command - 'tephra sololtr' started at: 09-08-2019 20:22:53.
Command - 'tephra sololtr' completed at: 09-08-2019 21:38:58.
Output files - /db/genome_v2_tephra_sololtrs.gff3
Output files - /db/genome_v2_tephra_sololtrs_rep.tsv
Output files - /db/genome_v2_tephra_sololtrs_seqs.fasta
Command - 'tephra illrecomb' started at: 09-08-2019 21:38:58.
Command - 'tephra illrecomb' completed at: 10-08-2019 00:05:24.
Output files - /db/genome_v2_tephra_illrecomb.fasta
Output files - /db/genome_v2_tephra_illrecomb_rep.tsv
Output files - /db/genome_v2_tephra_illrecomb_stats.tsv
Command - 'tephra findhelitrons' started at: 10-08-2019 00:05:24.
Command - 'tephra findhelitrons' completed at: 10-08-2019 04:30:59.
Output files - /db/genome_v2_tephra_helitrons.gff3
Output files - /db/genome_v2_tephra_helitrons.fasta
Command - 'tephra maskref' for Helitrons started at: 10-08-2019 04:31:01.
Command - 'tephra maskref' completed at: 10-08-2019 04:52:59. Final output file:
Output files - /db/genome_v2_tephra_masked3.fasta
Command - 'tephra findtirs' started at: 10-08-2019 04:52:59.
Command - 'tephra findtirs' completed at: 10-08-2019 05:32:57.
Command - 'tephra classifytirs' started at: 10-08-2019 05:32:57.
Tephra docker version was used:
tephra (Tephra) version 0.12.4 (/usr/local/bin/tephra)
Thanks for your help
Regards,
Jenny
This command works fine with one thread but issues arise when multiple threads are used.
I've installed tephra manually, maybe I did something wrong or missed something, but i had to install many modules and libs for using it:
sudo apt-get install libmoosex-perl libpath-class-perl libgsl-dev libmoose-perl
cpan Parallel::ForkManager
cpan Bio::GFF3::LowLevel
cpan YAML::Tiny
cpan Bio::DB::HTS::Kseq
cpan Log::Log4perl
cpan App::Cmd
cpan Path::Class
cpan Log::Any
cpan DateTime
cpan Lingua::EN::Inflect
cpan List::UtilsBy
cpan Number::Range
cpan Set::IntervalTree
cpan Log::Any::Adapter::Log4perl
I've also had a hard time installing htslib. This is why I'd suggest to use the docker option (in our case it was not possible at the time)
Hi Evan
I was wondering if you could explain me the LTR age output.
How is it calculate the age in each LTR family? The summary file have these columns:
Superfamily Family Family_size ElementID Divergence Age Ts:Tv
Copia RLC_family0 43 RLC_family0_exemplar 0.0471 2355000 3.2242
This particular family have 43 elements (family_size), however there is only one exemplar (ElementID) element. What is the Age value? Is the age from one element? Or the average for all 43 elements in that family? How is it calculate?
Best
Diego
There seems to be an incorrect number of LTR sequences being added to the exemplar file...looks like a bug.
Hi Evan,
Y ran tephra:
nohup tephra all -c tephra_config.yml &
since I want al types of TEs. I use a repbase.fasta from Solanum tuberosum for the repeatdb and left the others databases with the default options.
I'm having trouble to understand the differents output files, specially regarding the LTRs.
Could you explain me the differences between "elements" and "singleton"? Why are they in separated files?
What are the 2336 families and why the don't match with the elements or singletons?
this is from the log:
nano nohup.out
INFO - Results - Total number of Gypsy elements: 5003
...
INFO - Results - Number of Gypsy families: 2336
INFO - Results - Number of Gypsy elements in families: 2307
INFO - Results - Number of Gypsy singleton families/elements: 2696
INFO - Results - Number of Gypsy elements (for debugging): 5003
If I want it to use this information to search for copies in the genome, which set should I use to blastn them. Is one of these the consensus members of de different families?
And another issue is that I have 0 nonLTRs match, nor LINEs, or SINEs.
INFO - Command - 'tephra findnonltrs' started at: 05-11-2018 18:20:12.
[WARNING]: No non-LTR elements were found on the forward strand. Will search reverse strand.
[WARNING]: No non-LTR elements were found on the reverse strand.
[WARNING]: No non-LTR elements were found so none will be reported.
INFO - Command - 'tephra findnonltrs' completed at: 05-11-2018 22:27:29.
I know for a fact that there are SINEs and LINEs, actually the repbase from GIRI which I use have LINEs and SINEs.
Why do you thinks that happend?
Best
Diego
I've downloaded tephra_latest.sif and I'm running it on singularity 3.3.0. When I try a small test I get an immediate error:
> tephra all -c tephra_config.test1.yml
[ERROR]: 'debug' under 'all' is not defined after parsing configuration file.
This indicates there may be a blank line in your configuration file.
Please check your configuration file and try again. Exiting.
If I re-run the same command with no change to the config file I get a similar but different error:
> tephra all -c tephra_config.test1.yml
[ERROR]: 'trnadb' under 'all' is not defined after parsing configuration file.
This indicates there may be a blank line in your configuration file.
Please check your configuration file and try again. Exiting.
Each time I run the command I can get a different error with the same config. I've only made a few changes to the default yml, and I've attached the file (with a .txt on the end) in case I've done something wrong in there. Any ideas on what is going wrong?
The complete, LTR, and individual exemplar files are left behind right now from this command. Need to remove all but the LTRs and a single file of complete exemplars.
there is also an issue with printing an underscore instead of "-" for the strand.
Hi, I have executed succesfully the first (cpanm --installdeps .
) and second (perl Makefile.PL
) step. However, I obtain several erros when I execute the third step (make test
).
Output:
sudo make test
cp lib/Tephra/Genome/SoloLTRSearch.pm blib/lib/Tephra/Genome/SoloLTRSearch.pm
cp lib/Tephra/Classify/Fams/Cluster.pm blib/lib/Tephra/Classify/Fams/Cluster.pm
cp lib/Tephra.pm blib/lib/Tephra.pm
cp lib/Tephra/Genome/Unmask.pm blib/lib/Tephra/Genome/Unmask.pm
cp lib/Tephra/Command/findltrs.pm blib/lib/Tephra/Command/findltrs.pm
cp lib/Tephra/Command/findtirs.pm blib/lib/Tephra/Command/findtirs.pm
cp lib/Tephra/Annotation/Util.pm blib/lib/Tephra/Annotation/Util.pm
cp lib/Tephra/Alignment/Utils.pm blib/lib/Tephra/Alignment/Utils.pm
cp lib/Tephra/Config/Install.pm blib/lib/Tephra/Config/Install.pm
cp lib/Tephra/Genome/MaskRef.pm blib/lib/Tephra/Genome/MaskRef.pm
cp lib/Tephra/Command/illrecomb.pm blib/lib/Tephra/Command/illrecomb.pm
cp lib/Tephra/Annotation/Transfer.pm blib/lib/Tephra/Annotation/Transfer.pm
cp lib/Tephra/Genome/IllRecombination.pm blib/lib/Tephra/Genome/IllRecombination.pm
cp lib/Tephra/Classify/Fams.pm blib/lib/Tephra/Classify/Fams.pm
cp lib/Tephra/Command/classifyltrs.pm blib/lib/Tephra/Command/classifyltrs.pm
cp lib/Tephra/Analysis/Pipeline.pm blib/lib/Tephra/Analysis/Pipeline.pm
cp lib/Tephra/Command/all.pm blib/lib/Tephra/Command/all.pm
cp lib/Tephra/Classify/TIRSfams.pm blib/lib/Tephra/Classify/TIRSfams.pm
cp lib/Tephra/Classify/LTRSfams.pm blib/lib/Tephra/Classify/LTRSfams.pm
cp lib/Tephra/Command/findnonltrs.pm blib/lib/Tephra/Command/findnonltrs.pm
cp lib/Tephra/Command/classifytirs.pm blib/lib/Tephra/Command/classifytirs.pm
cp lib/Tephra/Annotation/FilterTandems.pm blib/lib/Tephra/Annotation/FilterTandems.pm
cp lib/Tephra/Command/age.pm blib/lib/Tephra/Command/age.pm
cp lib/Tephra/Annotation/MakeExemplars.pm blib/lib/Tephra/Annotation/MakeExemplars.pm
cp lib/Tephra/Command/maskref.pm blib/lib/Tephra/Command/maskref.pm
cp lib/Tephra/Config/Exe.pm blib/lib/Tephra/Config/Exe.pm
cp lib/Tephra/Config/Reader.pm blib/lib/Tephra/Config/Reader.pm
cp lib/Tephra/Command/findtrims.pm blib/lib/Tephra/Command/findtrims.pm
cp lib/Tephra/Genome/FragmentSearch.pm blib/lib/Tephra/Genome/FragmentSearch.pm
cp lib/Tephra/Classify/Any.pm blib/lib/Tephra/Classify/Any.pm
cp lib/Tephra/Classify/Role/LogResults.pm blib/lib/Tephra/Classify/Role/LogResults.pm
cp lib/Tephra/Command/reannotate.pm blib/lib/Tephra/Command/reannotate.pm
cp lib/Tephra/Hel/HelSearch.pm blib/lib/Tephra/Hel/HelSearch.pm
cp lib/Tephra/Command/findhelitrons.pm blib/lib/Tephra/Command/findhelitrons.pm
cp lib/Tephra/Command/sololtr.pm blib/lib/Tephra/Command/sololtr.pm
cp lib/Tephra/Command/findfragments.pm blib/lib/Tephra/Command/findfragments.pm
cp lib/Tephra/NonLTR/RunHMM.pm blib/lib/Tephra/NonLTR/RunHMM.pm
cp lib/Tephra/Role/Run/Any.pm blib/lib/Tephra/Role/Run/Any.pm
cp lib/Tephra/TIR/Role/Utils.pm blib/lib/Tephra/TIR/Role/Utils.pm
cp lib/Tephra/TRIM/TRIMSearch.pm blib/lib/Tephra/TRIM/TRIMSearch.pm
cp lib/Tephra/NonLTR/SeqUtils.pm blib/lib/Tephra/NonLTR/SeqUtils.pm
cp lib/Tephra/NonLTR/NonLTRSearch.pm blib/lib/Tephra/NonLTR/NonLTRSearch.pm
cp lib/Tephra/LTR/Role/Utils.pm blib/lib/Tephra/LTR/Role/Utils.pm
cp lib/Tephra/NonLTR/Postprocess.pm blib/lib/Tephra/NonLTR/Postprocess.pm
cp lib/Tephra/LTR/LTRSearch.pm blib/lib/Tephra/LTR/LTRSearch.pm
cp lib/Tephra/Role/Run/HelitronScanner.pm blib/lib/Tephra/Role/Run/HelitronScanner.pm
cp lib/Tephra/Role/Run/TephraCmd.pm blib/lib/Tephra/Role/Run/TephraCmd.pm
cp lib/Tephra/NonLTR/Role/PathUtils.pm blib/lib/Tephra/NonLTR/Role/PathUtils.pm
cp lib/Tephra/Role/Run/Blast.pm blib/lib/Tephra/Role/Run/Blast.pm
cp lib/Tephra/Role/GFF.pm blib/lib/Tephra/Role/GFF.pm
cp lib/Tephra/Role/Logger.pm blib/lib/Tephra/Role/Logger.pm
cp lib/Tephra/NonLTR/QValidation.pm blib/lib/Tephra/NonLTR/QValidation.pm
cp lib/Tephra/NonLTR/GFFWriter.pm blib/lib/Tephra/NonLTR/GFFWriter.pm
cp lib/Tephra/Role/Run/PAML.pm blib/lib/Tephra/Role/Run/PAML.pm
cp lib/Tephra/LTR/LTRRefine.pm blib/lib/Tephra/LTR/LTRRefine.pm
cp lib/Tephra/Stats/Age.pm blib/lib/Tephra/Stats/Age.pm
cp lib/Tephra/Role/Util.pm blib/lib/Tephra/Role/Util.pm
cp lib/Tephra/Role/File.pm blib/lib/Tephra/Role/File.pm
cp lib/Tephra/TIR/TIRSearch.pm blib/lib/Tephra/TIR/TIRSearch.pm
cp lib/Tephra/Role/Run/GT.pm blib/lib/Tephra/Role/Run/GT.pm
cp bin/tephra blib/bin/tephra
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/bin/tephra
cp bin/tephra-getphmm blib/bin/tephra-getphmm
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/bin/tephra-getphmm
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-config.t ......... 1/? # Testing Tephra 0.13.1, Perl 5.030000, /usr/bin/perl
t/00-config.t ......... ok
t/01-findltrs.t ....... 2/19 "blib/bin/tephra" unexpectedly returned exit value 1 at t/01-findltrs.t line 47.
# Looks like your test exited with 1 just after 2.
t/01-findltrs.t ....... Dubious, test returned 1 (wstat 256, 0x100)
Failed 17/19 subtests
t/02-classifyltrs.t ... 1/9 Can't stat t/test_data/ltr_family_domains: No such file or directory
at t/02-classifyltrs.t line 55.
# Looks like your test exited with 2 just after 1.
t/02-classifyltrs.t ... Dubious, test returned 2 (wstat 512, 0x200)
Failed 8/9 subtests
t/03-ltrage.t ......... ok
t/04-findtirs.t ....... 2/4 Can't open 't/test_data/ref_tirs.fasta' for reading: 'No such file or directory' at t/04-findtirs.t line 50
# Looks like your test exited with 1 just after 2.
t/04-findtirs.t ....... Dubious, test returned 1 (wstat 256, 0x100)
Failed 2/4 subtests
t/05-classifytirs.t ... 1/6 "blib/bin/tephra" unexpectedly returned exit value 255 at t/05-classifytirs.t line 50.
# Looks like your test exited with 255 just after 1.
t/05-classifytirs.t ... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 5/6 subtests
t/06-findtrims.t ...... ok
t/07-maskref.t ........ 1/4
# Failed test 'Can mask reference'
# at t/07-maskref.t line 42.
# Failed test 'Can mask reference'
# at t/07-maskref.t line 43.
# Failed test 'planned to run 4 but done_testing() expects 3'
# at t/07-maskref.t line 54.
# Looks like you failed 3 tests of 4.
t/07-maskref.t ........ Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/4 subtests
t/08-illrecomb.t ...... ok
t/09-sololtr.t ........ ok
t/10-findhelitrons.t .. ok
t/11-findnonltrs.t .... ok
t/12-tirage.t ......... ok
t/13-findfragments.t .. ok
t/14-all.t ............ ok
Test Summary Report
-------------------
t/01-findltrs.t (Wstat: 256 Tests: 2 Failed: 0)
Non-zero exit status: 1
Parse errors: Bad plan. You planned 19 tests but ran 2.
t/02-classifyltrs.t (Wstat: 512 Tests: 1 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 9 tests but ran 1.
t/04-findtirs.t (Wstat: 256 Tests: 2 Failed: 0)
Non-zero exit status: 1
Parse errors: Bad plan. You planned 4 tests but ran 2.
t/05-classifytirs.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 6 tests but ran 1.
t/07-maskref.t (Wstat: 768 Tests: 4 Failed: 3)
Failed tests: 2-4
Non-zero exit status: 3
Files=15, Tests=92, 27 wallclock secs ( 0.08 usr 0.02 sys + 32.77 cusr 1.83 csys = 34.70 CPU)
Result: FAIL
Failed 5/15 test programs. 3/92 subtests failed.
make: *** [Makefile:1122: test_dynamic] Error 255
How can I resolve this?
Thanks
Currently, the default is to use 12 CPUs which is not a good default. Need to set it to 1 to be nice.
There was a change to create a sub-directory for each fragment and these do not appear to be removed as the masking is progressing along...
In ages file I see things like:
RLC_family0_exemplar
And in the fasta files, I got
RLG_singleton_family1616_LTR_12347_chr07_42270149_42278820
RLC_singleton_family1616_TRIM_2991_chr04_13871214_13872432
So it is quite hard to connect those elements, how can I figure out which one is which?
Hi there,
I'm trying to install Tephra on a RHEL-based OS. I've downloaded the lastest version as per your Github instructions and I've installed all the core/per dependencies (I'm using perl v5.16.0 via perlbrew). However, I've run into this error when initiating the Makefile:
$ perl Makefile.PL
Generating a Unix-style Makefile
Writing Makefile for Tephra
Writing MYMETA.yml and MYMETA.json
=====> Configuring Tephra, this may take some time...
[ERROR]: move failed: Is a directory
It seems like it's happening shortly after the directory gt-1.5.10-Linux_x86_64-64bit-barebone (genome tools?) is unzipped but I can't find any reference to this in your makefiles.
Do you have any idea what might be causing this?
Thanks,
Grant
There are methods to annotate elements without the canonical coding domains in the expected order, though the unclassified count seems too high. Could be a bug or something that requires a different approach.
This is necessary so external programs can be found when running inside of containers.
In addition to the formatting issues, it appears the summary statistics are not being generated correctly. The results are only being shown for one family instead of all families.
Need to check for weeks, months in the logging step for the 'all' command.
Hi, I am triyng to install teprha, the firt step finish succesfully (perl Makefile.PL), but in the second step, I obtain this error:
make test
make: *** No rule to make target 'lib/Tephra.pm', needed by 'pm_to_blib'. Stop.
Can you help me with the isntallation??
Thanks
Sergio
I'm running tephra using potato genome
nohup tephra all -c tephra_config.yml &
This is the config file, the rest is as default
~/tephra/tephra-0.12.2/config$ cat tephra_config.yml
## For more information about this file, see:
## https://github.com/sestaton/tephra/wiki/Specifications-and-example-usage.
all:
- logfile: tephra_potato_genome.log
- genome: potato_dm_v404_all_pm_un.fasta
- outfile: potato_genome_transposons.gff3
- repeatdb: TEs_all_Repbase_St.fasta
- trnadb: TephraDB
- hmmdb: TephraDB
- threads: 14
- clean: YES
- debug: NO
- subs_rate: 1e-8
And this is the output with the error
tail -f nohup.out
INFO - Output files - /home/dzavallo/tephra/tephra-0.12.2/config/potato_dm_v404_all_pm_un_tephra_transposon_fragments.fasta
INFO - Command - Generating combined FASTA file of fragments and complete elements at: 06-11-2018 03:10:43.
INFO - Results - Finished generating combined FASTA file of fragments and complete elements at: 06-11-2018 03:10:49. Final output files:
INFO - Output files - potato_genome_transposons.fasta
INFO - Command - Generating combined GFF3 file at: 06-11-2018 03:10:49.
INFO - Results - Finished generating combined GFF3 file at: 06-11-2018 03:11:14. Final output files:
INFO - Output files - potato_genome_transposons.gff3
INFO - Command - Calculating global transposon family similarity at: 06-11-2018 03:11:14.
Use of uninitialized value $pid_sum in division (/) at /usr/local/share/perl/5.22.1/Tephra/Annotation/Util.pm line 378.
Illegal division by zero at /usr/local/share/perl/5.22.1/Tephra/Annotation/Util.pm line 378.
Currently not fast enough to complete in a reasonable time with genomes like sunflower. Need to make this command multi-threaded like other search strategies.
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