Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
Home Page: https://bionf.github.io/HaMStR/
License: GNU General Public License v3.0
Hello,
I followed the example provided in the README but I get the following error:
~/tools/HaMStR$ ./bin/oneSeq.pl -seqFile=data/infile.fa -seqid=P83876 -refspec=HUMAN@9606@1 -minDist=genus -maxDist=kingdom -coreOrth=5 -cleanup -global
Use of uninitialized value $force in numeric eq (==) at ./bin/oneSeq.pl line 1459.
MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY
Your sequence was named: nlTazcr
No FAS filter for core-orthologs set.
Annotation tools found in /home/ubuntu/annotation_fas!
#########################
--> Running annoFAS.pl
--> acquiring sequence lengths
...done: sequence lengths are calculated for input file.
--> starting: cast
--> starting: decodeanhmm
decodeanhmm 1.1f
Copyright (C) 1998 by Anders Krogh
Tue Feb 11 15:42:51 2020
Model in file "/home/ubuntu/annotation_fas/TMHMM/TMHMM2.0.model" parsed successfully.
--> starting: COILS2
1 sequences 142 aas 0 in coil
--> starting: signalp.pl
--> starting: seg
--> starting: pfam_scan.pl
Starting hmmscan now...
hmmscan finished.
Creating output file...
finished.
Deleting temporary output file...
--> starting: smart_scan_v4.pl
Starting hmmscan now...
hmmscan finished.
Creating output file...
finished.
Deleting temporary output file...
--> annotation finished.
tool start: 11/02/2020 15:42:51:0
tool end : 11/02/2020 15:42:54:0
#####################
Building up the taxonomy tree. Start 1581435774
--------------------- WARNING ---------------------
MSG: Could not merge the lineage of 40276 with the rest of the tree
---------------------------------------------------
Can't call method "add_Descendent" on an undefined value at /home/ubuntu/anaconda3/envs/hamstr/lib/site_perl/5.26.2/Bio/Tree/TreeFunctionsI.pm line 529.
Best,
Cata
Currently, the scoreThreshold is constitutively on. Implement a switch to de-activate it.
Hello,
I have been using this command for a long time, it woks well at HaMStR v.13.2.10. I installed HaMStR v.13.2.11 by ' conda install -c bionf hamstr' in a new system and then met this error. Is this a bug?
I am using a core_ortholog set trained by ourselves. Since input files are protein sequences, there are only *_prot.fa in blastdir. It seems that this hamstr doesn't recognize option "-protein".
Thank you!
command:
hamstr -hmmset=arthNreg2 -protein -cleartmp -cpu 12 -central -strict -refspec=drome_4 -sequence_file=Paranesidea_sp_croco.fas -taxon=Paranesidea_sp -representative
error:
checking for reference fasta files: Linked source for /home/depengli/HaMStR/blast_dir/drome_4/drome_4.fa not found in /mnt/d/Croco_hamstr_workdir! at /home/depengli/HaMStR/bin/hamstr line 1172.
uni-directional search using core-specific cutoff (bit, fas,...)
I add a my species to the reference databases use add addTaxon1s command, but it always show the "original sequence not found" when i choose the new species as ref-species with common "h1s --seqFile infile.fa --seqName test3 --refspec ARIFI@158543@1 --force", can you help me solved it ?
Since the matrix file does not support co-orthologs, we need to use the long format.
@holgerbgm you can use my script here to replace the current parseOneSeq.pl
parseOneSeq_mod.pl.txt
(remove the .txt extension after copying)
Usage:
perl parseOneSeq_mod.pl -i <path_to_hamstr_output> -o <job_name.profile>
where path_to_hamstr_output is the folder that contains *.extended.profile files.
Create gh-pages branch and move related documents (e.g. poster pdf files in www folder) to that branch. It will keep the master branch clean. See https://github.com/BIONF/phyloprofile-data/tree/gh-pages
Reading in large input files with FAS can take a moment. This is not critical when doing single FAS runs but might accumulate to larger runtimes during a oneseq run.
Adding a new input format that can be read faster might be something to work on for future releases, maybe even binary files for the oneseq library species.
Allow the ranking of hmmsearch hits by either global score (current implementation) or by the score of the best domain.
Hello
I tried running a loop for different proteins using the following command:
for PROTEIN in *fa; do oneSeq -seqFile=$PROTEIN -seqname=$PROTEIN -refspec=HUMAN@9606@1 -minDist=genus -maxDist=phylum -coreOrth=5 -cleanup -global -cpu=20 -countercheck; done
It runs with the first protein until it creates the *.extended.fa file and then it starts doing the second protein without any other output for the first protein. If I run the proteins one by one it works fine.
Best,
Cata
Bio folder are also exist in BioPerl/Bio folder.taxonomy downloaded from server still contains alt data. Will these old data be needed any where? The tar file taxdump.tar.gz can be also deleted.Dear Ingo,
During the annotation of one dataset I got the following error:
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
problem 1!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
problem 1!
Problem occurred: 2!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
Problem occurred: 2!
problem 1!
problem 1!
problem 1!
problem 1!
problem 1!
Problem occurred: 2!
problem 1!
problem 1!
Problem occurred: 2!
Problem occurred: 2!
finished.
Deleting temporary output file...
--> annotation finished.
tool start: 23/02/2020 13:13:19:0
tool end : 24/02/2020 4:12:16:0
#####################
Any clues on what it means ?
Thanks!
Best,
Cata
Hello
I installed HaMStR using conda. I ran the setup_hamstr | tee log.txt and it appears that there was no error during the setup.
I tried running the sample file but I get the following error.
There was an error running HaMStR v.13.2.10
VERSION: HaMStR v.13.2.10
HOSTNAME lmu-thesis1
USER DEFINED PARAMTERS (inc. default values)
-append: not set
-blastpath: /home/ubuntu/tools/HaMStR/blast_dir/
-checkCoorthologsRef: not set
-cleartmp: not set
-concat: not set
-est: not set
-eval_blast: 0.0001
-eval_hmmer: 0.0001
-filter: F
-hit_limit: not set
-hmm: not set
-hmmpath: /home/ubuntu/tools/HaMStR/core_orthologs/
-hmmset: ppkdOcJ
-intron: k
-longhead: not set
-nonoverlapping_cos: not set
-outpath: /home/ubuntu/tools/HaMStR/output/ppkdOcJ
-protein: 1
-rbh: not set
-refspec: HUMAN@9606@1
-relaxed: not set
-representative: not set
-reuse: not set
-sequence_file: DROME@[email protected]
-show_hmmsets: not set
-sort_global_align: not set
-strict: not set
-taxon: DROME@7227@1
-ublast: 0
INFILE PROCESSING
A modified infile DROME@[email protected] already exists. Using this one
Newlines from the infile have been removed
CHECKING FOR PROGRAMS
check for blastp succeeded
check for hmmsearch succeeded
CHECKING FOR HMMs
running HaMStR with all hmms in /home/ubuntu/tools/HaMStR/core_orthologs//ppkdOcJ/hmm_dir
check for /home/ubuntu/tools/HaMStR/core_orthologs//ppkdOcJ/ppkdOcJ.fa succeeded
CHECKING TAXON NAME
using default taxon DROME@7227@1 for all sequences
CHECKING FOR REFERENCE TAXON
Reference species for the re-blast: HUMAN@9606@1
CHECKING FOR BLAST DATABASES
check for /home/ubuntu/tools/HaMStR/blast_dir//HUMAN@9606@1/HUMAN@9606@1 succeeded
CHECKING FOR REFERENCE FASTA FILES
Removing line breaks from /home/ubuntu/tools/HaMStR/genome_dir/HUMAN@9606@1/HUMAN@[email protected].
FATAL: Problems running the script nentferner.pl
PROGRAM OPTIONS
hmmsearch will run with an e-value limit of 0.0001
re-blast hit_limit: none applied
Blast will run with an evalue limit of 0.0001
check for low complexity filter setting succeeded. Chosen value is F
HaMStR was called without the -representative option. More than one ortholog may be identified per core-ortholog group!Evaluation of predicted HaMStR orthologs.
Error: Could not find /home/ubuntu/tools/HaMStR/data/ppkdOcJ.extended.fa
Do you know what could be causing this error ?
Thank you!
Regards,
Cata
I noticed that the FAS calculation was not immediately cancelled even if there is no annotation available for one proteins (either seed or query), which takes unnecessary time for whatever processing. I have some (thousand) cases where it took minutes to do something and gave me nothing :-)
I suggest to check for the availability of the annotations before doing any further processing and give a proper error message to say e.g. which protein has not been annotated.
The data download for oneseq has an older version of the pfam db (version 30.0) newest version is (32.0)
Hello
I am manually creating a new data set. In the step 6 (Create the annotation files for your taxon with the provided perl script) I get the following error:
Can't exec "/home/ubuntu/annotation_fas/CAST/cast": No such file or directory at /home/ubuntu/anaconda3/envs/hamstr/lib/python3.8/site-packages/greedyFAS/annoFAS.pl line 909.
Use of uninitialized value $castOut in scalar chomp at /home/ubuntu/anaconda3/envs/hamstr/lib/python3.8/site-packages/greedyFAS/annoFAS.pl line 910.
Use of uninitialized value $castOut in concatenation (.) or string at /home/ubuntu/anaconda3/envs/hamstr/lib/python3.8/site-packages/greedyFAS/annoFAS.pl line 911.
I used the following command:
annoFAS --fasta=/home/ubuntu/tools/HaMStR/genome_dir/TEST@00001@1/TEST@[email protected] --path=/home/ubuntu/tools/HaMStR/weight_dir --name=TEST@00001@1
It seems that CAST is not compiled to work with our system. I couldn't find the CAST v1.0 on their webpage.
Best,
Cata
Provided taxonomy data together with the preprocessed genome data can lead to the using of invalid NCBI taxonomy, which causes problem when visualizing output using PhyloProfile. I suggest we should:
The same can be applied for annotation tools (pfam, smart, tmhmm,...). But it requires automatic tests for testing the compatible of the new version with the current data (for example check if any using functions got deprecated from the new version).
Only the preprocessed genome data (blast_dir, genome_dir, weight_dir) should be downloaded from our server.
When calculating the FAS score, oneseq extracts the the feature architecture of the found ortholog from the species input creating a lot of temporary files. Because of the seed_id/query_id options of FAS, this is no longer neccessary and should be changed.
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