dfam-consortium / tetools Goto Github PK

View Code? Open in Web Editor NEW

78.0 78.0 16.0 164 KB

Dfam Transposable Element Tools Docker container.

License: Creative Commons Zero v1.0 Universal

Dockerfile 50.28% Shell 49.72%

tetools's People

Contributors

Stargazers

Watchers

Forkers

wangpanqiao shulp2211 ravindra-raut pedrobdfp xyl012 xyz0o biofalcon hlkfoz wtroy2 mechealeth albertrockg akanksha-nbri

tetools's Issues

forksys: Program terminated by a signal 9.

................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
forksys: Program terminated by a signal 9.
The executing command was: /opt/RepeatMasker/ProcessRepeats -lib RM_919634.MonOct101112052022/consensi.fa.classified -orifile GCA_018340775.1_ASM1834077v1_genomic.fna -maskSource /PBIO2/Taxus/communicationbiology/RM_3932828.ThuOct131112242022/GCA_018340775.1_ASM1834077v1_genomic.fna /PBIO2/Taxus/communicationbiology/RM_3932828.ThuOct131112242022/GCA_018340775.1_ASM1834077v1_genomic.fna.cat.gz
Singularity> ls CommunicationBioQC.tar.gz Cplant.03.nni
CommunicationBioQCtest Cplant.03.nog
Cplant-families.fa Cplant.03.nsq
Cplant-families.stk Cplant.nal
Cplant-rmod.log Cplant.translation
Cplant.00.nhr Crun.out
Cplant.00.nin GCA_018340775.1_ASM1834077v1_genomic.fna
Cplant.00.nnd RM_919634.MonOct101112052022
Cplant.00.nni SRR14089425
Cplant.00.nog SRR14089426
Cplant.00.nsq SRR14089427
Cplant.01.nhr SRR14089428
Cplant.01.nin SRR14089429
Cplant.01.nnd SRR14089430
Cplant.01.nni SRR14089431
Cplant.01.nog SRR14089432
Cplant.01.nsq SRR14089433
Cplant.02.nhr SRR14089434
Cplant.02.nin SRR14089435
Cplant.02.nnd SRR14089436
Cplant.02.nni SRR14453978
Cplant.02.nog SRR14453979
Cplant.02.nsq SRR14865989
Cplant.03.nhr commfastq
Cplant.03.nin repeatmaskout
Cplant.03.nnd
Singularity> RepeatMasker -nolow -no_is -norna -pa 16 -lib RM_919634.MonOct101112052022/consensi.fa.classified -dir repeatmaskout GCA_018340775.1_ASM1834077v1_genomic.fna

Above is what I got after running for a long time. I thinks something is broken. Can you help me figure it out? Thanks.

reasonaTE "https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE"

Dear jebrosen

Thank you for tools. If I use this docker image, can I run the following comment

RepeatModeler -help
BuildDatabase -name demo_index -engine ncbi demo.fasta
RepeatModeler -engine ncbi -pa 10 -database demo_index
RepeatMasker -help
RepeatMasker -pa 10 demo.fasta

Because I want to combine the results with _reasonaTE to get GFF3.

Please give me your suggestion.

Perhaps CONS-Dfam_3.2 missing from container?

Describe the bug
Not sure, but maybe the RepeatMasker Libraries directory is missing a file/dir like CONS-Dfam_3.2? Should this work, or is it misguided?

To Reproduce
Using LIBDIR, which is simply a writable, private copy of /opt/RepeatMasker/Libraries. The command seems to fail because it's trying to access Libraries files it expects, but which do not exist.

$ LIBDIR=/projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries  singularity exec --
bind=/projects,/packages docker://dfam/tetools:1.2 RepeatMasker  -species liliopsida empty.fa
RepeatMasker version 4.1.1
Search Engine: NCBI/RMBLAST [ 2.10.0+ ]

Using Master RepeatMasker Database: /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/RepeatMaskerLib.h5
  Title    : Dfam
  Version  : 3.2
  Date     : 2020-07-02
  Families : 6,953

Species/Taxa Search:
  Liliopsida [NCBI Taxonomy ID: 4447]
  Lineage: root;cellular organisms;Eukaryota;Viridiplantae;
           Streptophyta;Streptophytina;Embryophyta;Tracheophyta
  9 families in ancestor taxa; 0 lineage-specific families

Building general libraries in: /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general
RepeatMasker::createLib(): Error invoking /opt/rmblast/bin/makeblastdb on file /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general
/is.lib.

Expected behavior
Not very familiar with RM, but was expecting it to try to extract/build the sub-library for the named species. ??

Alternatively, is there any reasonably simple way to add this to my writable copy?

Host system (please complete as much of the following information as you can find out):

RHEL 7.8
Singularity 3.3.0-1
Container image 1.2 (same behavior with latest)

Same genome assembly, different RM versions: output comparison

Describe the bug
I noticed that using the newer version of rmblast 2.10.0+ and RepeatMasker4.1.1 returns less known TE families but more unknown TEs

To Reproduce
commands used with the previous version of RMblastn and RepeatMasker4.0.1 without the container:

/RepeatModeler.v2.0.1/BuildDatabase -name drosophila_XXX -engine ncbi ../../5_freeze_v0/monCan3F9.ctg.v0.fa
RepeatModeler -engine ncbi -pa 64 -database drosophila_XXX
queryRepeatDatabase.pl -species drosophila > drosophila.repeat.lib
cat consensi.fa.classified drosophila.repeat.lib > drosophila.monCan3F9.repeat.lib
/RepeatMasker-4.1.0/RepeatMasker -e ncbi -pa 64 -s -lib drosophila.monCan3F9.repeat.lib -dir repeatmasker_final -xsmall -html -gff ../../5_freeze_v0/monCan3F9.ctg.v0.fa

commands used with the newer singularity container version:

singularity exec --bind $PWD:$PWD ../RepeatModeler/tetools.sif BuildDatabase -name monCan3F9 monCan3F9.fa
singularity exec --bind $PWD:$PWD ../RepeatModeler/tetools.sif RepeatModeler  -database monCan3F9 -pa 40 -LTRStruct 
singularity> famdb.py -i Libraries/RepeatMaskerLib.h5 families --format fasta_name --include-class-in-name --ancestors --descendants 7215 > dorosphila.rm.fa
singularity > famdb.py -i Libraries/RepeatMaskerLib.h5 families --format fasta_name --include-class-in-name --ancestors --descendants 32281 > drosophila.subgenus.rm.fa
 cat monCan3F9-families.fa drosophila.rm.fa drosophila.subgenus.rm.fa > drosophila.monCan3F9_newlib.fa
singularity exec --bind $PWD:$PWD ../RepeatModeler/tetools.sif RepeatMasker -lib drosophila.monCan3F9_newlib.fa  -dir repeatmasker_new  monCan3F9.fa -engine ncbi -pa 40 -nolow

Expected behavior
I expected to recover higher TEs than the older version since the total size of my new lib was even bigger in the newer version (8,23 MG) than the older one (7,12 MG) and the input file is the same. Instead the total number of masked bases and known TEs are lower and only unknown TEs are higher.

below is the comparison of output tables:

p.s. I have tried masking with several different combinations; running RM_4.1.1; with only 7215 library, and with the RM4.0.1 output library, running RM_4.0.1 with the new (4.1.1) library... I could recover slightly more unclassified TEs but the known families are always less than old approach.

p.s.s I have added and merged the RepBase library to the RepeatMasker_4.1.1 inside the container, but it doesn't indicate it in the output table file, I don't know if it is normal?

Feature request: Make the Docker image multi-platform

Hi,

I'd like to request to make the Docker image multi-platform.
Currently https://hub.docker.com/r/dfam/tetools/tags are only for linux/amd64.
Could you please add linux/arm64 to the supported platforms ?

The task should be (relatively) easy by using docker buildx instead of docker build. I'd be glad to help if the feature is approved!

Thank you!

BuildDatabase step problem

Hello, TEtools team

Describe the bug
BuildDatabase command dont work well this time.

To Reproduce
BuildDatabase -name JEC21 /data/JEC21/db/JEC21.fasta

Expected behavior
BuildDatabase: Cannot open file JEC21.translation
I'm confused because I can run this last time. I just use a new *.fasta file. And im sure that the file is same with the one as before.

Host system (please complete as much of the following information as you can find out):

uname -a
Linux bbc0927150e3 5.10.47-linuxkit # 1 SMP Sat Jul 3 21:51:47 UTC 2021 x86_64 GNU/Linux
lsb_release -a
No LSB modules are available
Distributor ID: Denian
Description: Debian GNU/Linux 9.13(stretch)
Release:9.13 Codename:stretch
docker --version
20.10.10.build b485636

Looking for your reply
Best Regards!

famdef and eleredef steps fail when using the docker image on a Mac

Hi :-)

Hope this finds you well! Thank you so much for the tool.

I successfully downloaded the docker image onto my Mac as per the instructions on the README page. I also manage to execute the BuildDatabase command fine, however when I try to execute the RepeatModeler command (-database <name_of_database -pa 10 -LTRStruct ), the code fails. So far it has failed twice and I'm re-running it again in case it solves itself :-)

The first time the error stated: "famdef failed. Exit code 1024"
The second time, after re-running with the -recover_Dir option: "eleredef failed. Exit code 11"

The log files appear intact, and the only clue that something is wrong comes from the Exit code details.

Have you encountered this issue with a Mac? Or is it simply a matter of trying it a couple more times to see if it runs to completion? I should say that both times it failed after round_3, so I could still use the files in this folder or from the earlier rounds, but I just wanted to see if I can run it to completion.

Any advice would be greatly appreciated!

Cheers,
kevin

Not sure how I should deal with the forecast results and the results of the existing database

Hello! Thank you very much for developing such good software. Recently, I have a few unsure questions that I would like to ask you.
We assembled a genome and we made predictions through RepeatModeler software. We ran the RepeatMasker software using the predicted set of repeat sequences (***-family. fa) and found that the repeat sequence of the genome was as high as 38.75 %. This may be right. However, we also used the repetitive sequences of existing species based on dfam and repbase databases, and we found that the repetitive sequences reached 41.31%. I also tried to merge the prediction results with the results of the database and found that the repetitive sequence was as high as 44.71%. This result was much higher than our expectations. This may be wrong.
I am not sure which result we should use for subsequent genome annotation analysis, I would like to ask you.
Looking forward to hearing from you!

RepeatMasker "forksys: Program terminated by a signal 7"

Hi all,

I'm running RepeatMasker using TETools through the singularity wrapper script. And it seems to be terminating at the same spot. I get the following error message while it is generating the output:

forksys: Program terminated by a signal 7. The executing command was: /opt/RepeatMasker/ProcessRepeats -lib consensi.fa.classified -gff -poly -u -source -html -xm -orifile assembly_v1.0.fasta -maskSource /home/roger/Analysis/Assembly_v1.0/RM_1798.MonMar92212332020/assembly_v1.0.fasta -xsmall /home/roger/Analysis/Assembly_v1.0/RM_1798.MonMar92212332020/assembly_v1.0.fasta.cat.gz

I'm using this command:
RepeatMasker -pa 30 -gff -html -xsmall -lib consensi.fa.classified -xm -u -poly -q -source assembly_v1.0.fasta

any ideas what the problem could be?

RepeatMasker genome1.fa -lib library.fa -pa 8

$ RepeatMasker genome1.fa [-lib library.fa] [-pa 8]
Hello, the example you put on the website, I don't know what this - lib library. fa refers to?
If I have an assembled pig genome, how should I set up library.fa in this place?

Singularity Container Issues

Having some issues running the container via singularity. RepeatModeler works perfectly fine, but RepeatMasker crashes.

josephguhlin@biochemcompute1 /V/a/d/g/j/a/m/M/assemblies> bash repeatmasker.sh                                                                                                                                                                (base) 
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LC_TIME = "en_NZ.UTF-8",
        LC_MONETARY = "en_NZ.UTF-8",
        LC_ADDRESS = "en_NZ.UTF-8",
        LC_TELEPHONE = "en_NZ.UTF-8",
        LC_NAME = "en_NZ.UTF-8",
        LC_MEASUREMENT = "en_NZ.UTF-8",
        LC_IDENTIFICATION = "en_NZ.UTF-8",
        LC_NUMERIC = "en_NZ.UTF-8",
        LC_PAPER = "en_NZ.UTF-8",
        LANG = "C"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
RepeatMasker version 4.1.0
Search Engine: NCBI/RMBLAST [ 2.10.0+ ]
Master RepeatMasker Database: /opt/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: CONS-Dfam_3.1 )
Custom Repeat Library: ./MH-families.fa



analyzing file mhype.assembly.fa

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-1.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-2.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-3.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-4.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-5.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-6.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-7.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-8.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-10.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-9.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-11.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-12.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-13.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-14.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-15.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-16.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 1 ) [ 255,, 72915]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-1.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 9 ) [ 255,, 67740]...
WARNING: Retrying batch ( 10 ) [ 255,, 33838]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 13 ) [ 255,, 38600]...

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-9.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 2 ) [ 255,, 48537]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-10.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 12 ) [ 255,, 75686]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-13.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 3 ) [ 255,, 74351]...

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: Retrying batch ( 16 ) [ 255,, 47190]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-2.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-12.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-3.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-16.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 5 ) [ 255,, 12318]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-5.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 14 ) [ 255,, 47190]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-14.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 6 ) [ 255,, 50273]...
WARNING: Retrying batch ( 4 ) [ 255,, 70609]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 7 ) [ 255,, 50274]...

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-6.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-4.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-7.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 8 ) [ 255,, 71856]...
WARNING: Retrying batch ( 11 ) [ 255,, 33838]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 15 ) [ 255,, 47190]...

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-8.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-11.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-15.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 9 ) [ 255,, 67740]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 1 ) [ 255,, 72915]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-9.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-1.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 2 ) [ 255,, 48537]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 13 ) [ 255,, 38600]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-2.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: Retrying batch ( 10 ) [ 255,, 33838]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-13.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-10.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 5 ) [ 255,, 12318]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 6 ) [ 255,, 50273]...
WARNING: Retrying batch ( 16 ) [ 255,, 47190]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 3 ) [ 255,, 74351]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-5.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-6.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 7 ) [ 255,, 50274]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-16.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 14 ) [ 255,, 47190]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-3.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-7.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-14.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 11 ) [ 255,, 33838]...

Checking for E. coli insertion elements
WARNING: Retrying batch ( 4 ) [ 255,, 70609]...
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-11.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-4.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 12 ) [ 255,, 75686]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-12.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 8 ) [ 255,, 71856]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-8.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.
WARNING: Retrying batch ( 15 ) [ 255,, 47190]...

Checking for E. coli insertion elements
WARNING: The search engine returned an error (255, status = 255 )
Engine parameters: /opt/rmblast/bin/rmblastn  -num_alignments 9999999 -db /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/is.lib -query /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020/mhype.assembly.fa_batch-15.masked -gapopen 12 -gapextend 2 -complexity_adjust  -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8  -min_raw_gapped_score 17 -dust no  -num_threads 4  -matrix identity.matrix 
A search phase could not complete on this batch.
The batch file will be re-run and if possible the
program will resume.


FATAL ERROR: RepeatMasker giving up. One or more
batches failed!  Unfortunately this type of error
cannot be recovered from. Please submit the following
details to the feedback page at the repeatmasker
website:

       http://www.repeatmasker.org

RepeatMasker Version: 4.1.0
Library Version: CONS-Dfam_3.1
Search Engine: ncbi [ 2.10.0+ ]
Command Line: /opt/RepeatMasker/RepeatMaskermhype.assembly.fa -e ncbi -pa 16 -xsmall -html -gff -lib ./MH-families.fa
Batch Number: 3
Disk Space:
Filesystem        1K-blocks         Used   Available Use% Mounted on
archive        507380835584 427940422680 79440412904  85% /Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies

System Memory:
MemTotal:       1056114176 kB
MemFree:        865090320 kB
MemAvailable:   879192996 kB
Cached:         127629024 kB
SwapCached:            0 kB
SwapTotal:      45855740 kB
SwapFree:       45855740 kB
Further details about this problem may be found in
the directory: **/Volumes/archive/deardenlab/guhlin/johnskelly/annotations/microctonus/MH/assemblies/RM_108032.MonFeb30920372020**

/V/a/d/g/j/a/m/M/a/RM_75721.MonFeb30911162020> cat ncResults-1580674289-99751.err                                                                                                                                (base) 
Error: mdb_dbi_open: MDB_NOTFOUND: No matching key/data pair found

TRF path error while running a Docker

Dear,
i was trying to install Repeatmodeler2 via docker container. but i am facing a TRF PATH error problem. i am attaching a screenshot of that, please help me to solve this issue.

Default output directory cannot be modified

Describe the bug
Hi,

I cannot change the default output directory when mounting the image in singularity. It will always write to home. There should be an option to specify the output directory and/or the working directory. LOCAL is the local scratch directory. Even though I specifically try to overide the home directory, it will always write to the home directory. Please advice

To Reproduce

CWD=$(pwd)
cp repeatmodeler.sif ${LOCAL}
cp ${MYFASTA} ${LOCAL}
cd ${LOCAL}

export HOME=${LOCAL}
HOME=${LOCAL}
MOUNTDIR=/data
singularity instance start --bind $(pwd):${MOUNTDIR} repeatmodeler.sif repeatmodeler

SPECIES=myspecies

singularity exec instance://repeatmodeler export HOME=${MOUNTDIR}
singularity exec instance://repeatmodeler BuildDatabase -name ${SPECIES} ${MOUNTDIR}/$MYFASTA

expected behavoir
The user should be able to specify the output and working directories.

This is using singularity 3.7.1

RepeatClassifier does not recognize the LIBDIR variable shown in the README

I followed instructions on https://github.com/Dfam-consortium/TETools#readme to add Repbase. After I set LIBDIR to the new Libraries directory, can RepeatModeler/RepeatClassifier pick up the LIBDIR value and use Repbase? I read the code, it seems that RepeatClassifier still uses the old /opt/RepeatMasker/Libraries/RepeatMasker.lib file.

runcoseg.pl -d -m 50 -c ALU.cons -s ALU.seqs -i ALU.ins

After l done the RepeatMasker genome1.fa [-lib library.fa] [-pa 8].
How can I use the next command? runcoseg.pl -d -m 50 -c ALU.cons -s ALU.seqs -i ALU.ins
This is the result document I have at present！
genome1.fa genome1.fa.cat.gz genome1.fa.masked genome1-families.fa genome1-families.stk genome1.fa.out genome1.fa.tbl genome1.nhr genome1.nin genome1.nnd genome1.nni genome1.nog genome1.nsq genome1.translation
thank you!

addRepbase.pl: no such file

Describe the bug

(dfam-tetools /data/fungi/db)$ tar -x -f RepBaseRepeatMaskerEdition-20181026.tar.gz
(dfam-tetools /data/NJ103/db)$ ls Libraries/
README.RMRBSeqs  RMRBSeqs.embl 
(dfam-tetools /data/NJ103/db)$ addRepBase.pl -lib Libraries/
Rebuilding RepeatMaskerLib.h5 master library
  - Read in 49011 sequences from Libraries//RMRBSeqs.embl
    Reading metadata database...EMBL::_parseFromFile() Unable to open RepeatMasker/EMBL file Libraries//RMRBMeta.embl: No such file or directory

I use TEtools 1.7 for docker.
Looking forward your reply!
Best Wishes!

accessing util scripts within singularity container?

Sorry for the silly question -- Is there a way to access the utilities scripts available in RepeatMasker within the singularity container? eg. calcDivergenceFromAlign.pl etc

Docker build from Dockerfile fails: no source files were specified

I'm trying to build the container from the Dockerfile, however I keep getting the following:

Sending build context to Docker daemon  7.168kB
Step 1/28 : FROM debian:9 AS builder
 ---> 5ddf6ebdcdb4
Step 2/28 : RUN apt-get -y update && apt-get -y install     curl gcc g++ make zlib1g-dev libgomp1     perl     python3-h5py     libfile-which-perl     libtext-soundex-perl     libjson-perl liburi-perl libwww-perl
 ---> Using cache
 ---> 9778373078cc
Step 3/28 : COPY src/* /opt/src/
COPY failed: no source files were specified

To Reproduce
docker build - < Dockerfile

Docker version: Docker version 20.10.10, build b485636

Main workstation running Ubuntu 20.04 LTS.

Include ps in container for nextflow?

Hi there, just a quick note that it would be nice to have ps within the TE Tools Docker container, as that allows for better compatability with Nextflow. See here:
nextflow-io/nextflow#1289 (comment)

Recovering run that failed while executing LTR_retriever

Used version: TETools git commit bf94dc1

Hi, I ran RepeatModeler on my assembly through the Docker container and it failed while executing LTR_retriever. The LTR_retriever.log file in the LRET_49037.WedFeb260356552020 contained the following error: RepeatMasker is not running properly!. As I have managed to complete a run of RepeatMasker through the Docker container in the past, I believe that a simple rerun of RepeatModeler from that point may solve the issue.

However, I am unable to rerun RepeatModeler using the --recoverDir option, as it tells me that the working directory appears to contain a successful run. Do you have any suggestions on how I could finish this run without starting from scratch?

Below you will find the LTR_retriever.log file, please let me know if you need any additional details from my side.

LTR_retriever.log

Dfam Browse download

Additional context
Dear developers,
I'm working with the gff3 of the C. elegans annotation in worm base parasite,
I got the rows of repetitive elements that look like this:

I RepeatMasker repeat_region 1622 1744 431 + . Target=LONGPAL1 136 261 +

I would like to get the annotation of these repeats at the class or family level using the "target" information.
I noticed that most of the targets have a hit in Dfam Browse however my gff3 has 116933 rows, Is it possible to download the table of Dfam browse?

ERRO[10728] error waiting for container: unexpected EOF

l print the "RepeatModeler -pa 10 -database Test -LTRStruct >& 1.run.out"

##The log showed "Comparison Time: 00:07:52 (hh:mm:ss) Elapsed Time, 1368539 HSPs Collected

RECON: Running imagespread..
RECON Elapsed: 00:00:02 (hh:mm:ss) Elapsed Time
RECON: Running initial definition of elements ( eledef )..
RECON Elapsed: 00:00:14 (hh:mm:ss) Elapsed Time
RECON: Running re-definition of elements ( eleredef ).."

ERRO[10728] error waiting for container: unexpected EOF

l do not know how to slove it, can you help me?
Thank you!

RepeatMasker returning impossible coordinates

Describe the bug

Many repeat coordinates hits in the ".out" file are longer than the query repeat.
For example, the line below is data is from the ".out", which a hit is to a consensus repeat (DR0021180) which is 3217bp long, yet says it's a hit to 4804-5218:

15803 11.6 1.8 1.5 ctg_1 35113158 35113313 (105938908) + DR0021180 LINE/RTE-BovB 4804 5218 (195) 43774

However the likely corresponding line from the ".align" file do not have this issue:
15803 7.67 1.17 0.28 ctg_1 35110690 35112821 (105939400) DR0021180#LINE/RTE-BovB 1 2151 (1066) m_b606s001i18 43774

Of note there is are hits from other BovBs which overlap the coordinates(from .align):

1366 29.30 3.74 8.29 ctg_1 35112325 35113180 (105939041) BovB_Ml#LINE/RTE-BovB 456 1275 (174) m_b606s001i19 43774 2098 17.41 0.51 1.81 ctg_1 35112819 35113210 (105939011) DR0087524#LINE/RTE-BovB 1444 1830 (438) m_b606s001i21 43774 520 31.22 9.94 4.46 ctg_1 35112938 35113299 (105938922) DR0143386#LINE/RTE-BovB 4838 5218 (195) m_b606s001i22 43774 714 17.39 5.07 0.00 ctg_1 35113176 35113313 (105938908) DR0020736#LINE/RTE-BovB 2466 2610 (1) m_b606s001i23 43774

The library used was from

https://www.dfam.org/releases/Dfam_3.5/families/Dfam.h5.gz

To Reproduce
Steps to reproduce the behavior, including the full command line used to start the container and any commands run inside the container.

RepeatMasker -species reptilia -pa 32 genome.fasta

Expected behavior

The repeats coordinates should not be outside that of the reference sequence.

Host system (please complete as much of the following information as you can find out):
Linux 5.4.0-94-generic #106-Ubuntu
The above data is from an manual install from the RepeatMasker website, but I have had the same issue on multiple other reptile genomes using RepeatMasker installed from the docker container

Additional context
This is on a species of snake. I have an assumption this may be due to a growing level of redundancy with the reptile Dfam sequences, along with misclassified sequences.

LTRStruct can't find RMblast engine

Hello,

I ran singularity exec repmasker.simg RepeatModeler -database mydb -LTRStruct. I have a families.fa file, but my output log says the following:

LTR Structural Analysis

Running LtrHarvest... : 00:00:30 (hh:mm:ss) Elapsed Time
Running Ltr_retriever...LTRPipeline: No results after LTR_Retriever filtering.
LTRPipeline Time: 00:00:35 (hh:mm:ss) Elapsed Time

RepeatClassifier Version 2.0.1

Search Engine = rmblast

Looking for Simple and Low Complexity sequences..
Looking for similarity to known repeat proteins..
Looking for similarity to known repeat consensi..
Classification Time: 00:15:23 (hh:mm:ss) Elapsed Time

The LTR_retriever.log says the following:
Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

I'm not sure (a) how the program can't find a dependency within a container or (b) how rmblast worked for RepeatClassifier but not the LTR pipeline.

Host system
-linux x86.64
-singularity 3.6.4
-container installed as follows:
singularity build repmasker.simg docker://dfam/tetools:latest
(I couldn't get a successful install with the wrapper script)

Thank you

> The combine is a very confusing place for us. What causes such a deviation?

Error in Job submitting of Slurm on cluster : if it is possible to disable the need for an internet connection

Dear Authors of program.

Thanks for very nice program.
Now I run RepeatModeler with Dfam TE Tools Container. ( with using Singularity Container)
Job can work directly on command line. But When I summit it as job, it failed.

My Job:
(
#!/bin/bash
#SBATCH --time=1:00:00 # hh:mm:ss
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=4000 # megabytes
singularity run -B /scratch/ulg/bbasv/daomhai/Docker docker://dfam/tetools:latest RepeatModeler -database Catfish22 -engine ncbi -pa 32 )

The result in Slurm:
(
time="2021-12-26T19:39:42+01:00" level=warning msg=""/run/user/3003415" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/3003415: no such file or directory: Trying to pull image in the event that it is a public image."
FATAL: Unable to handle docker://dfam/tetools:latest uri: failed to get checksum for docker://dfam/tetools:latest: error pinging docker registry registry-1.docker.io: Get https://registry-1.docker.io/v2/: dial tcp: lookup registry-1.docker.io on [::1]:53: read udp [::1]:47463->[::1]:53: read: connection refused. )

I contact with manager of Cluster he said that compute nodes does not have a direct internet access**.
So I would like to ask the authors of the program if it is possible to disable the need for an internet connection when running
job program on cluster ??
Or do you have other advices ??

Thank you for your help and I look forward to hearing your advice.

Thanks in advance
Sincerely yours
Hai

How to make and use a RepeatMasker custom library inside the singularity container?

Hi,

I have installed the Rmodeler2 singularity container and I have merged the RepBase library to the RMasker library which is integrated inside the container using below instruction:

# Navigate to an appropriate directory that is persistent outside the container
$ cd /work

# Make a copy of RepeatMasker's Libraries directory here
$ cp -r /opt/RepeatMasker/Libraries/ ./

# Extract RepBase (the .tar.gz file unpacks files into Libraries/)
$ tar -x -f /work/path/to/RepBaseRepeatMaskerEdition-#######.tar.gz

# Run the 'addRepBase.pl' script (part of the RepeatMasker package) to merge the databases,
# specifying the custom Libraries directory.
$ addRepBase.pl -libdir Libraries/

# Run RepeatMasker with the LIBDIR environment variable set
$ export LIBDIR=/path/to/Libraries

I have run the Repeatmodeler on a non-model organism's genome assembly:
singularity exec --bind $PWD:$PWD ./tetools.sif RepeatModeler -database monCan3F9 -pa 40 -LTRStruct

now before running the RepeatMasker, I want to merge the monCan3F9-families.fa with the "Dfam.h5" library, how should I do that?

Also, regarding your new RM version, should I utilize the "queryRepeatDatabase" option to separately drag Drosophila library or not? because I saw it in older versions of RM but couldn't find in your current documentation with the container.

this is how inside my Library looks like now.

Add TRF

TRF is now open source: https://github.com/Benson-Genomics-Lab/TRF

It would be convenient if it were included in the TE Tools container image.

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.