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mpdunne / orthofiller

OrthoFiller: Identifying missing annotations for evolutionarily conserved genes.
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Several issues #8

Open danshu opened 7 years ago

danshu commented 7 years ago

I have used orthofiller and have following issues:

  1. "0.1. Checking installed programs" failed to test some shell commands I'm sure that I have these shell commands but this step somewhat failed. So that I do not do into this step.

  2. In the step "1.2. Preparing gtf files for Augustus training", I have errors: ERROR: illegal character '.' found in integer conversion of string ".". Exiting... ERROR: illegal character '.' found in integer conversion of string ".". Exiting... I have googled it and it seems that this may be related to bedtools.

  3. For Orthogroup statistics, number of genes seems to be number of isoforms. Is orthofiller aware of and able to deal with gene structures with mutiple isoforms?

Best, Quan

mpdunne commented 7 years ago

Hi Quan,

Please see responses in >>green below!

All the best,

Michael

From: danshu [mailto:notifications@github.com] Sent: 17 August 2017 03:00 To: mpdunne/orthofiller orthofiller@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [mpdunne/orthofiller] Several issues (#8)

I have used orthofiller and have following issues:

  1. "0.1. Checking installed programs" failed to test some shell commands I'm sure that I have these shell commands but this step somewhat failed. So that I do not do into this step.

This sounds like an issue with the software checks (better safe than sorry!) Could you let me know what shell and system you are using and what the error message is from this step?

1.

In the step "1.2. Preparing gtf files for Augustus training", I have errors:

ERROR: illegal character '.' found in integer conversion of string ".". Exiting... ERROR: illegal character '.' found in integer conversion of string ".". Exiting... I have googled it and it seems that this may be related to bedtools.

Could you send me a copy of the gtf files you’re using?

  1. For Orthogroup statistics, number of genes seems to be number of isoforms. Is orthofiller aware of and able to deal with gene structures with mutiple isoforms?

Currently OrthoFiller doesn’t distinguish genes from transcripts. I might add an option in for this later on – the only problem is that this requires a decision on which transcript to take as the primary transcript, which may not always be transcript 1. I would suggest that if you only want one transcript from each gene to be considered, include only these in your input gtf file.

Best, Quan

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danshu commented 7 years ago

Hi Michael，

I'm using bash and Ubuntu. Error messages: Test can run "man sed" - failed ERROR: Cannot run sed Please check sed is installed and that the executables are in the system path Test can run "man echo" - failed ERROR: Cannot run echo Please check echo is installed and that the executables are in the system path ...

  1. I have tested with the example data and the same error occurs on the example dataset Ashgo1. I'm using bedtools v2.24.0.

Best. Quan

mpdunne commented 7 years ago

[https://tr.cloudmagic.com/h/v6/emailtag/tag/2.0/1503044007/362f86978213108f86a5a8b78262f84e/3/c27e319654c1956ad6e4517247af6c32/6a6cf39013ed6ea33c0c7d9060753fda/3b71bdd096a4081c34819cd55715f1cf/newton.gif]

What is he output if you type "man echo" and "man sed" into the command line?

On Fri, Aug 18, 2017 at 5:03am, danshu notifications@github.com<mailto:notifications@github.com> wrote:

Hi Michael，

I'm using bash and Ubuntu. Error messages: Test can run "man sed" - failed ERROR: Cannot run sed Please check sed is installed and that the executables are in the system path Test can run "man echo" - failed ERROR: Cannot run echo Please check echo is installed and that the executables are in the system path ...

  1. I'm testing now with the example data to find out whether it is really caused by my gtf file.

Best. Quan

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danshu commented 7 years ago

e.g. man sed: SED(1) User Commands SED(1)

NAME sed - stream editor for filtering and transforming text

SYNOPSIS sed [OPTION]... {script-only-if-no-other-script} [input-file]...

14zac2 commented 3 years ago

Hi there - I also had this issue. I was trying to run OrthoFiller using nohup, and it was not working for the life of me. Turns out, all I had to do was add < /dev/null to the end of my nohup command, so it ended up looking like nohup ./run_ortho.sh >& nohup.out < /dev/null where run_ortho.sh was my own personal command line argument to run OrthoFiller (e.g. python ~/bin/orthofiller/orthofiller.py -i ./target_species.tdv -r ./reference_species.tdv -o ortho_output -c 15 --fulloutput).