Error in 'Alignment' module with MAFFT alignment

[IdoBar]

Hi,

I read your recent publication and I'm really interested in trying out AliTV, but I can't get it to work with my data.
I got 8 viral genomes in FASTA format which were aligned by MAFFT.
I added the following lines to the yaml file:

---
alignment:
    program: importer
    parameter:
        - "../WSSV_genomes_MAFFT_alignment.fasta"

genomes:
  - name: AF332093.3
    sequence_files:
      - WSSV_genome_AF332093.3.fasta
  - name: AF369029.2
    sequence_files:
      - WSSV_genome_AF369029.2.fasta
  - name: AF440570.1
    sequence_files:
      - WSSV_genome_AF440570.1.fasta
  - name: JX515788.1
    sequence_files:
      - WSSV_genome_JX515788.1.fasta
  - name: KR083866.1
    sequence_files:
      - WSSV_genome_KR083866.1.fasta
  - name: KT995470.1
    sequence_files:
      - WSSV_genome_KT995470.1.fasta
  - name: KT995471.1
    sequence_files:
      - WSSV_genome_KT995471.1.fasta
  - name: KT995472.1
    sequence_files:
      - WSSV_genome_KT995472.1.fasta
  - name: KU216744.1
    sequence_files:
      - WSSV_genome_KU216744.1.fasta
output:
  conf: conf.json
  data: data.json
  filter: filter.json

And ran it with the following command:
perl -Ilib ~/etc/tools/Annotation/AliTV-perl-interface-1.0.2/bin/alitv.pl --overwrite --project WSSV WSSV.yml
However, I get the following error:

Use of uninitialized value in subroutine entry at /home/ibar/etc/tools/Annotation/AliTV-perl-interface-1.0.2/bin/../lib/AliTV/Alignment.pm line 262, <GEN9> line 55170.
FATAL - unable to create features at /home/ibar/etc/tools/Annotation/AliTV-perl-interface-1.0.2/bin/../lib/AliTV/Alignment.pm line 305

When I tried to use lastz to align the sequences (giving the fasta files as input, without a yaml file), it produced a different error:
FATAL - Unable to load alignment module 'AliTV::Alignment::lastz' at /home/ibar/etc/tools/Annotation/AliTV-perl-interface-1.0.2/bin/alitv.pl line 117.

Thank you, Ido

[greatfireball]

Dear Ido,

thanks for the bug report. I was able to reproduce the error with the MAFFT import of the sequences, but I need to go deeper to solve that puzzle. Nevertheless, I tried to run the lastz mode and it worked for me. I downloaded the virus sequences from NCBI and used the following command to run the script:

alitv.pl AF332093.3.fasta AF369029.2.fasta AF440570.1.fasta JX515788.1.fasta KR083866.1.fasta KT995470.1.fasta KT995471.1.fasta KT995472.1.fasta KU216744.1.fasta

Please ensure to use the complete path to alitv.pl or that it is available via PATH. Additionally, the lastz binary have to be in PATH. Please find the output as attached zip file.

Best Frank

PS: Uploader does not accept my zip, so I uploaded the json to https://pastebin.com/dl/5QBGt249

[IdoBar]

Thanks Frank,

I'll have a look at that json file.
The lastz mode still isn't working for me ()giving the same error as mentioned above).
I'm using lastz (version 1.02.00 built 20100112 with gcc-4.8.5), alitv.pl is available in the PATH, I'm using Perl v5.27 (tried unsuccessfuly with 5.22 before), with BioPerl-1.007001

Thanks, Ido

[greatfireball]

It seems that something went wrong during installation... The message unable to locate the AliTV::Alignment::lastz module is unexpected. Inside your installation folder (~/etc/tools/Annotation/AliTV-perl-interface-1.0.2/) should be a folder lib/AliTV/Alignment/containing the files importer.pm, lastz.pm, and template.pm. Obviously, the importer.pm was found (MAFFT import), therefore lastz.pm should be found too...
Please check if the file exists and let me know.

And a short update on the MAFFT issue, multiple alignments are currently not supported (see #33). That might cause the issue. I will try to fix that and will let you know.

Thanks for your help,
Frank

[IdoBar]

Hi Frank,

All the three modules are there (importer.pm, lastz.pm, template.pm).
I'm using the latest GitHub version.

Thanks, Ido

[greatfireball]

Hi Ido,
sry for the delay, I am still not sure about the issue with the lastz module, nevertheless, I am working on the MAFFT import now. Import is working, but I still have in issue with name mapping (see issue #144). It will be finished by the end of this week, therefore AliTV will support multiple alignments by the end of this week. Hope, that is still okay for you.
Best,
Frank

[IdoBar]

Thanks Frank, That would actually be best cause I have a particular alignment that I want to visualize. Thanks, Ido

…

On Jun 27, 2017 6:28 PM, "Frank Förster" ***@***.***> wrote: Hi Ido, sry for the delay, I am still not sure about the issue with the lastz module, nevertheless, I am working on the MAFFT import now. It will be finished by the end of this week, therefore AliTV will support multiple alignments by the end of this week. Hope, that is still okay for you. Best, Frank — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#136 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APbRHK_rhXt46BZWuS0M3aWCBNBEzPqnks5sIL0cgaJpZM4N6wbN> .