Dear iTAK developpers,
When I run perl iTAK.pl Atha_seq, the following error occurred,

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:438
STACK: Bio::PrimarySeqI::translate /usr/local/share/perl5/Bio/PrimarySeqI.pm:656
STACK: Bio::SeqUtils::translate_3frames /usr/local/share/perl5/Bio/SeqUtils.pm:374
STACK: Bio::SeqUtils::translate_6frames /usr/local/share/perl5/Bio/SeqUtils.pm:400
STACK: main::itak_identify /home/wzy/biosoft/iTAK/iTAK.pl:190
STACK: /home/wzy/biosoft/iTAK/iTAK.pl:41

How can I resolve it? Thanks a lot.

Hi,
I try to analyze transcription factors and kinase family-related genes using the transcriptome data. I have the unigenes file in the fasta format. I am getting an error like this.

Error: Sequence file ./Trinity.fasta_temp/protein_seq.fa is empty or misformatted

[ERR]cmd: /home/raman/bin/iTAK/bin/hmmscan --acc --notextw --cpu 20 -o ./Trinity.fasta_temp/protein_seq.pfam.hmmscan.txt /home/raman/bin/iTAK/database/Tfam_domain.hmm ./Trinity.fasta_temp/protein_seq.fa

How to solve this issue.

I am looking forward to hearing from you.

With best regards,
Raman. G

Dear iTAK developpers,

The argument -o seems not to be taken into account to specify the output directory (release 1.7.a).

I fixed this bug just byt adding the line $output_dir = $$options{'o'} if (defined $$options{'o'}); at lines 68 and 165.

Sincerely,

Sebastien

Dear developer,

Thank you for your excellent work! And I found that the conda distribution seems missing:

Could not solve for environment specs
The following package could not be installed
└─ itak does not exist (perhaps a typo or a missing channel).

If this problem solved, please let me know.

Best regards,

Andrew

dear friend:
I run the command with "python ~/iTAK-2.0.2/iTAK.py -p 3 -o hap1.itak -c hap1.pep1" , but its error with show "ValueError: could not convert string to float:"

its very weird, when I run the test fasta in your software, its ok ,and have the result, so I think maybe the software need the special format, so I use the seqkit seq to generate the new file, but its also error. so maybe the id was error , the original was like "Cannabis1G00001.t1", modified "Cannabis1G00001t1", its still error. other ways to try, I extract the 100 sequences to run, its down. but when extract the 200 sequences, still error .
so how handle with this question.
thank you

    if hits and score and hits_s and score_s:

<<<<<<< HEAD
rule_id = compare_rule(hits, score, hits_s, score_s, tf_rule)

    rule_id = compare_rule(hits, score, hits_s, score_s, tf_rule)

7fd4519

Thank you for developing the excellent iTAK software! After using it, I have some questions that I would like to ask for your guidance:

(1) The reference database used by iTAK has not been updated for a long time. If I want to manually update the database, how can I do it?

(2) If it is possible to construct the database by myself, can I use the data from animalTFDB to build another reference database and make iTAK suitable for identifying transcription factors in animals?

Looking forward to your reply. Thank you!