PhyloPhlAn error

[beeo...@berkeley.edu]

Hi,

I installed PhyloPhlAn with correct versions of all the required softwares(muscle, FastTree and usearch) and python modules. However, I still see this error. Is there anything wrong?

error message:

./phylophlan.py -u my_genomes
Generating data/ppa.wdb (usearch indexed DB)... Done!
Looking for PhyloPhlAn proteins in input faa files
Starting data/my_genomes/C08.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/C08.b6o -query input/my_genomes/C08.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/C08.b6o generated!
Starting data/my_genomes/A36.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A36.b6o -query input/my_genomes/A36.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A36.b6o generated!
Starting data/my_genomes/A56.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A56.b6o -query input/my_genomes/A56.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A56.b6o generated!
Starting data/my_genomes/B44.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B44.b6o -query input/my_genomes/B44.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B44.b6o generated!
Starting data/my_genomes/D24.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D24.b6o -query input/my_genomes/D24.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D24.b6o generated!
Starting data/my_genomes/E23.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/E23.b6o -query input/my_genomes/E23.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/E23.b6o generated!
Starting data/my_genomes/A13.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A13.b6o -query input/my_genomes/A13.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A13.b6o generated!
Starting data/my_genomes/A20.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A20.b6o -query input/my_genomes/A20.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A20.b6o generated!
Starting data/my_genomes/B20.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B20.b6o -query input/my_genomes/B20.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B20.b6o generated!
Starting data/my_genomes/B36.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B36.b6o -query input/my_genomes/B36.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B36.b6o generated!
Starting data/my_genomes/E60.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/E60.b6o -query input/my_genomes/E60.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/E60.b6o generated!
Starting data/my_genomes/E68.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/E68.b6o -query input/my_genomes/E68.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/E68.b6o generated!
Starting data/my_genomes/E70.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/E70.b6o -query input/my_genomes/E70.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/E70.b6o generated!
Starting data/my_genomes/A28.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A28.b6o -query input/my_genomes/A28.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A28.b6o generated!
Starting data/my_genomes/B48.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B48.b6o -query input/my_genomes/B48.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B48.b6o generated!
Starting data/my_genomes/A31.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A31.b6o -query input/my_genomes/A31.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A31.b6o generated!
Starting data/my_genomes/A41.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A41.b6o -query input/my_genomes/A41.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A41.b6o generated!
Starting data/my_genomes/D82.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D82.b6o -query input/my_genomes/D82.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D82.b6o generated!
Starting data/my_genomes/D36.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D36.b6o -query input/my_genomes/D36.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D36.b6o generated!
Starting data/my_genomes/D25.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D25.b6o -query input/my_genomes/D25.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D25.b6o generated!
Starting data/my_genomes/A54.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A54.b6o -query input/my_genomes/A54.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A54.b6o generated!
Starting data/my_genomes/B07.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B07.b6o -query input/my_genomes/B07.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B07.b6o generated!
Starting data/my_genomes/A32.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A32.b6o -query input/my_genomes/A32.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A32.b6o generated!
Starting data/my_genomes/A02.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A02.b6o -query input/my_genomes/A02.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A02.b6o generated!
Starting data/my_genomes/B62.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B62.b6o -query input/my_genomes/B62.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B62.b6o generated!
Starting data/my_genomes/A57.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A57.b6o -query input/my_genomes/A57.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A57.b6o generated!
Starting data/my_genomes/B15.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B15.b6o -query input/my_genomes/B15.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B15.b6o generated!
Starting data/my_genomes/B09.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B09.b6o -query input/my_genomes/B09.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B09.b6o generated!
Starting data/my_genomes/D69.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D69.b6o -query input/my_genomes/D69.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D69.b6o generated!
Starting data/my_genomes/D07.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D07.b6o -query input/my_genomes/D07.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D07.b6o generated!
Starting data/my_genomes/D17.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D17.b6o -query input/my_genomes/D17.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D17.b6o generated!
Starting data/my_genomes/D57.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D57.b6o -query input/my_genomes/D57.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D57.b6o generated!
Starting data/my_genomes/B13.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B13.b6o -query input/my_genomes/B13.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B13.b6o generated!
Starting data/my_genomes/A14.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A14.b6o -query input/my_genomes/A14.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A14.b6o generated!
Starting data/my_genomes/B58.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/B58.b6o -query input/my_genomes/B58.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/B58.b6o generated!
Starting data/my_genomes/D59.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D59.b6o -query input/my_genomes/D59.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D59.b6o generated!
Starting data/my_genomes/A33.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A33.b6o -query input/my_genomes/A33.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A33.b6o generated!
Starting data/my_genomes/A19.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/A19.b6o -query input/my_genomes/A19.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/A19.b6o generated!
Starting data/my_genomes/D88.b6o...


usearch -quiet -wdb data/ppa.wdb -blast6out data/my_genomes/D88.b6o -query input/my_genomes/D88.faa -evalue 1e-40

---Fatal error---
Cannot open data/ppa.wdb, errno=2 No such file or directory
data/my_genomes/D88.b6o generated!
All usearch runs performed!
Mapping finished in 3 secs.

All alignments already computed!
Aligning finished in 0 secs (3 total time).

Traceback (most recent call last):
  File "./phylophlan.py", line 803, in <module>
    aln_merge(projn,pars['integrate'])
  File "./phylophlan.py", line 525, in aln_merge
    v.id = k
AttributeError: 'str' object has no attribute 'id'

Thanks!

[Francesco Asnicar]

Hello,

it seems to me that there is something wrong with usearch, actually. Can you provide the output of the "usearch -version" command?

Also, can you post the content of the "data/" folder in PhyloPhlAn?

Many thanks,

Francesco

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[beeo...@berkeley.edu]

Hi, 

Thanks for your response. usearch --version output is here:

usearch v5.2.32

content of the data/ folder is here:

my_genomes

ppaalns

ppafull.aln.faa

ppafull.aln.faa.tar.bz2

ppafull.orgs2prots.txt

ppafull.orgs2prots.txt.tar.bz2

ppafull.tax.txt

ppafull.up2prots.txt

ppafull.up2prots.txt.tar.bz2

ppafull.xml

ppaull.xml.tar.bz2

ppa.seeds.faa

ppa.seeds.faa.tar.bz2

Thanks.

[Francesco Asnicar]

Hi, it seems that the usearch version is the correct one, but in your data folder the "ppa.wdb" file is missing.

Can you execute the following commands:

    ./phylophlan.py -c my_genomes > ppa_my_genome.log 2>&1

    ./phylophlan.py --cleanall >> ppa_my_genome.log 2>&1

    ./phylophlan.py -u my_genomes >> ppa_my_genome.log 2>&1

The first two commands are used to clean the project files, and the latter simply execute PhyloPhlAn on your data. When executing PhyloPhlAn after the cleaning, it should re-generate the files in the data folder, hoping that this time the "ppa.wdb" file will be generated.

At the end of the three commands, if you can send me back the "ppa_my_genome.log" file, I can have a look if the commands executed correctly.

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/84fff4c7-dd04-4ad2-a700-d1f6122b5f74%40googlegroups.com.

[beeo...@berkeley.edu]

Thanks for your help, Francesco.

After executing the commands you mentioned and executing ./phylophlan.py -u my_genomes, the following errors appear:

$ ./phylophlan.py -u my_genomes

Generating data/ppa.wdb (usearch indexed DB)... Done!

All usearch runs already performed!
Mapping finished in 0 secs.

All alignments already computed!
Aligning finished in 0 secs (0 total time).

Traceback (most recent call last):
  File "./phylophlan.py", line 803, in <module>
    aln_merge(projn,pars['integrate'])
  File "./phylophlan.py", line 525, in aln_merge
    v.id = k
AttributeError: 'str' object has no attribute 'id'

$ ls data
my_genomes               ppafull.orgs2prots.txt          ppafull.xml
ppaalns                  ppafull.orgs2prots.txt.tar.bz2  ppafull.xml.tar.bz2
ppafull.aln.faa          ppafull.up2prots.txt            ppa.seeds.faa
ppafull.aln.faa.tar.bz2  ppafull.up2prots.txt.tar.bz2    ppa.seeds.faa.tar.bz2

Thanks,
HC

[Francesco Asnicar]

This is strange, also because from the "ls" you posted the "ppa.wdb" is not present.

Can you send your input folder "my_genomes", so that I can run PhyloPhlAn and try to reproduce your error?

Many thanks,

Francesco

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[luisa....@scilifelab.se]

Any updates on this front?

I have recently installed a fresh build of Phylophlan on a new machine and am having the same problem, even when running example_corynebacteria.

This machine has several versions of usearch installed, but I aliased "usearch" as version 5.2.32 before trying to run phylophlan. This should be enough, right?

All the best,
Luisa

[Francesco Asnicar]

Hi Luisa,
unfortunately I am not able to reproduce the same error you're having.

Can you please run the following commands and then send me back the "ppa_my_genome.log" file?

./phylophlan.py -c example_corynebacteria > ppa_my_genome.log 2>&1

./phylophlan.py --cleanall >> ppa_my_genome.log 2>&1

./phylophlan.py -u example_corynebacteria >> ppa_my_genome.log 2>&1

It would be great if you could also send me the result from the ls command in the "data/" folder before and after executing the last of the three PhyloPhlAn executions above.

Many thanks,
Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/9efe56d8-e62e-48d8-9912-961e67708068%40googlegroups.com.

[luisa....@scilifelab.se]

So, unfortunately I been mucking about too much and decided to start from a fresh build, so the first 2 commands weren't applicable... I started therefore directly from the -u example:

$ usearch --version
usearch v5.2.32
$ ls data
ppaalns  ppafull.aln.faa.tar.bz2  ppafull.orgs2prots.txt.tar.bz2  ppafull.tax.txt  ppafull.up2prots.txt.tar.bz2  ppafull.xml.tar.bz2  ppa.seeds.faa.tar.bz2
$  ./phylophlan.py -u example_corynebacteria >> ppa_my_genome.log 2>&1
$ ls data
example_corynebacteria  ppafull.aln.faa          ppafull.orgs2prots.txt          ppafull.tax.txt       ppafull.up2prots.txt.tar.bz2  ppafull.xml.tar.bz2  ppa.seeds.faa.tar.bz2
ppaalns                 ppafull.aln.faa.tar.bz2  ppafull.orgs2prots.txt.tar.bz2  ppafull.up2prots.txt  ppafull.xml                   ppa.seeds.faa

The log is attached.

Thanks for the prompt replies!
/Luisa

[Francesco Asnicar]

Hi Luisa,

from the log you sent me back it seems that your problem is due to usearch. The file "ppa.wdb" in the "data/" folder, in fact, is not present from the last ls command you posted in your e-mail.

Can you try execute the following command (it is the command that PhyloPhlAn should execute) and send me back the output?

usearch --makewdb data/ppa.seeds.faa --output data/ppa.wdb

Can you also verify, after the command executed, if the "ppa.wdb" file is present in the "data/" folder?

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/288b590a-4cb8-45d5-a5d3-982da8e70103%40googlegroups.com.

[luisa....@scilifelab.se]

Hi Francesco,

Usearch behaves normally:

$ usearch --makewdb data/ppa.seeds.faa --output data/ppa.wdb > usearch.log
usearch v5.2.32 (32-bit, 2.0Gb avail / 132Gb RAM)
(C) Copyright 2010-11 Robert C. Edgar, all rights reserved.
Licensed to: luisa....@scilifelab.se

00:02 197Mb  100.0% Reading data/ppa.seeds.faa
00:02 197Mb 292.4k sequences                 
00:07 235Mb  100.0% Building index (pass 1)
00:39 868Mb  100.0% Building index (pass 2)
00:40 868Mb  100.0% Writing index         
00:40 868Mb Buffers             
00:41 885Mb  100.0% Seqs

$ ls data/
example_corynebacteria  ppafull.aln.faa.tar.bz2         ppafull.tax.txt               ppafull.xml          ppa.seeds.faa.tar.bz2
ppaalns                 ppafull.orgs2prots.txt          ppafull.up2prots.txt          ppafull.xml.tar.bz2  ppa.wdb
ppafull.aln.faa         ppafull.orgs2prots.txt.tar.bz2  ppafull.up2prots.txt.tar.bz2  ppa.seeds.faa


However, attempting to run the example after that still fails:

$ ./phylophlan.py -u example_corynebacteria

Looking for PhyloPhlAn proteins in input faa files

Starting data/example_corynebacteria/C_accolens_ATCC49725.b6o...

Invalid command line
Unknown option wdb
Starting data/example_corynebacteria/C_genitalium_ATCC33030.b6o...

Invalid command line
Unknown option wdb
Starting data/example_corynebacteria/C_kroppenstedtii_DSM44385.b6o...

Invalid command line
Unknown option wdb
Starting data/example_corynebacteria/C_pseudotuberculosis_I19.b6o...

Invalid command line
Unknown option wdb
All usearch runs performed!

Traceback (most recent call last):

  File "./phylophlan.py", line 792, in <module>
    faa2ppafaa( inps, pars['nproc'], projn )
  File "./phylophlan.py", line 291, in faa2ppafaa
    for l in open(dat_fol+i+".b6o").readlines()):
IOError: [Errno 2] No such file or directory: 'data/example_corynebacteria/C_accolens_ATCC49725.b6o'


So it seems like Phylophlan somehow fails to find usearch internally, although it is there. Could I tweak the phylophlan code to give it the absolute path to my usearch? I couldn't find which line in the code that would be.

Thanks again,
Luisa

[Francesco Asnicar]

Hi Luisa,

I'm not sure what is not working, mainly because I'm not able to reproduce the error you got.
I got a similar error only if I use a newer version of usearch, but with the 5.2.32 version everything is working fine, in my case.

Can you try these two commands and then send me back the "usearch.log" file?
usearch --makewdb data/ppa.seeds.faa --output data/ppa.wdb > usearch.log 2>&1
usearch -wdb data/ppa.wdb -blast6out data/example_corynebacteria/C_accolens_ATCC49725.b6o -query input/example_corynebacteria/C_accolens_ATCC49725.faa -evalue 1e-40 >> usearch.log 2>&1

Many thanks,
Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/07eb7dd7-1c59-41f1-a97a-62677bc6b269%40googlegroups.com.

[luisa....@scilifelab.se]

So turns out aliasing doesn't work in non-interactive sessions (cf http://unix.stackexchange.com/questions/1496/why-doesnt-my-bash-script-recognize-aliases)

I just had to make a system-wide soft-link from usearch to usearch5 and warn all other users to please state their desired version explicitly when using usearch directly. Hopefully this won't create conflict with other third-party pipelines in the future.

Thanks again for your help and persistence in troubleshooting

/Luisa

[Francesco Asnicar]

Thanks Luisa for finding the issue!

Is this also applying to your case Heejung Cho?

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/400ac52b-e7e4-40e1-b637-ca759e2f4a3e%40googlegroups.com.

[GIRIJA KAUSHAL]

Hello Francesco,

I am facing the same issue as discussed above. Being new to this, I am not able to understand how this is solved and how this will work in my machine.

Please guide me. Check the attachment for log file.

[Francesco Asnicar]

Hello,

The error you encountered is most likely due to a wrong version of usearch. Can you please check that the usearch you've installed in your system is the version 5.2.32 (you can have a look at the wiki on Bitbucket https://bitbucket.org/nsegata/phylophlan/wiki/Home, in particular at the "External Software Dependencies" section).

The problem described earlier on this thread was referring to a problem with usearch which ended up not to be a problem with the version of usearch, but with the fact that userach was exported as an alias and this is not working in an interactive bash.

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/9da09ef3-fc4c-4388-b073-a8bcd3f142ec%40googlegroups.com.

[GIRIJA KAUSHAL]

Thank you for quick reply.

I installed usearch v10.0.240 that seems to be the latest version. So, do I need to re-install the version 5.2.32?

I am getting the same error as reported in this thread earlier so I thought it to be the same issue. What can I do to check if usearch installed in my system is not exported as an alias?

[Francesco Asnicar]

Hi,

Yes, as reported in the "External Software Dependencies" of the PhyloPhlAn wiki (https://bitbucket.org/nsegata/phylophlan/wiki/Home):

"""

External Software Dependencies

 * muscle version v3.8.31 or higher must be present in the system path and called "muscle"

 * usearch version v5.2.32 (notice that version 6 is currently NOT supported) must be present in the system path and called "usearch"

 * FastTree version 2.1 or higher must be present in the system path and called "FastTree"

 * Biopython it is a PyPhlAn dependency, actually, but used inside PhyloPhlAn

"""

So, please make sure you have all the dependencies in your system and they are installed as written above.

The "alias problem" reported earlier in this thread cloud arise when in renaming the external dependencies of PhyloPhlAn (for instance usearch must be present in the system path and called userach), instead of actual renaming the executables, you create an alias that is not exported in non-interactive shells. You can have a look at the link Luisa posted earlier for more details (http://unix.stackexchange.com/questions/1496/why-doesnt-my-bash-script-recognize-aliases).

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/5c752827-6682-4fac-87b5-89dafb8ee7f8%40googlegroups.com.

[GIRIJA KAUSHAL]

Thank you for quick reply.

I installed usearch v10.0.240 that seems to be the latest version. So, do I need to re-install the version 5.2.32?

I am getting the same error as reported in this thread earlier so I thought it to be the same issue. What can I do to check if usearch installed in my system is not exported as an alias?

Best regards

With best regards

Girija

JRF (DST INSPIRE FELLOW)

Center of Innovative and Applied Bioprocessing (CIAB)

(Department of Biotechnology, Government of India)
C-127, 2nd floor, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali
Punjab, India-160071

Mob: +91 7529009198

Email: gir...@ciab.res.in, girija...@gmail.com

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[GIRIJA KAUSHAL]

Thank you Francesco for your valuable suggestions.

I reinstalled usearch and it worked well without any error. But,phylophlan doesn't provide any newwick tree as output. The two output files I got by PhyloPhlan are attached as: aln.fna and aln_stats.tsv

Then, I tried running FastTree indepentently (attached as FastTree). But I still cannot find any tree build. Please find its log file and output file attached as: LM_phylophlan.txt and LM_phylophlan

Please suggest me some solution.

I also tried Mega tool to build a tree but it is also not working.

Kindly suggest me some solution.

On Sunday, April 8, 2018 at 3:10:54 AM UTC+5:30, GIRIJA KAUSHAL wrote:

Thank you for quick reply.

I installed usearch v10.0.240 that seems to be the latest version. So, do I need to re-install the version 5.2.32?

I am getting the same error as reported in this thread earlier so I thought it to be the same issue. What can I do to check if usearch installed in my system is not exported as an alias?

Best regards

With best regards

Girija

JRF (DST INSPIRE FELLOW)

Center of Innovative and Applied Bioprocessing (CIAB)

(Department of Biotechnology, Government of India)
C-127, 2nd floor, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali
Punjab, India-160071

Mob: +91 7529009198

Email: gir...@ciab.res.in, girijaka...@gmail.com

[Francesco Asnicar]

Hi Girija,

It's strange that you didn't get an output tree from PhyloPhlAn, if you can provide the full command line and the output from PhyloPhlAn, I can have a look at them. One thing that can be the problem here is that you maybe run PhyloPhlAn on the same input several times (for fixing the usearch problem, I guess) without cleaning the temporary file PhyloPhlAn creates at each run, could be that the case?

In any case, the output from your manual run of FastTree (which is very close to the command that PhyloPhlAn will execute, except for some params) seems correct to me, "LM_phylophlan" seems a correct newick file, can you please double check or am I missing something?

Many thanks,

Francesco

On Mon, Apr 9, 2018 at 9:24 AM GIRIJA KAUSHAL <girija...@gmail.com> wrote:

Thank you Francesco for your valuable suggestions.

I reinstalled usearch and it worked well without any error. But,phylophlan doesn't provide any newwick tree as output. The two output files I got by PhyloPhlan are attached as: aln.fna and aln_stats.tsv

Then, I tried running FastTree indepentently (attached as FastTree). But I still cannot find any tree build. Please find its log file and output file attached as: LM_phylophlan.txt and LM_phylophlan

Please suggest me some solution.

I also tried Mega tool to build a tree but it is also not working.

Kindly suggest me some solution.

On Sunday, April 8, 2018 at 3:10:54 AM UTC+5:30, GIRIJA KAUSHAL wrote:

Thank you for quick reply.

I installed usearch v10.0.240 that seems to be the latest version. So, do I need to re-install the version 5.2.32?

I am getting the same error as reported in this thread earlier so I thought it to be the same issue. What can I do to check if usearch installed in my system is not exported as an alias?

Best regards

With best regards

Girija

JRF (DST INSPIRE FELLOW)

Center of Innovative and Applied Bioprocessing (CIAB)

(Department of Biotechnology, Government of India)
C-127, 2nd floor, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali
Punjab, India-160071

Mob: +91 7529009198

Email: gir...@ciab.res.in, girija...@gmail.com

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/9da09ef3-fc4c-4388-b073-a8bcd3f142ec%40googlegroups.com.
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[GIRIJA KAUSHAL]

Thank you for so quick reply. I don't know about visualizing newick file. If it seems correct to you then I feel like checking it but Please tell me how can I visualize it as tree?

I had cleaned all files each time I ran PhyloPhlAn but still I will check that again.

Please tell me how to visualize Tree format of LM_phylophlan  as it appears just like  a text file.

With best regards

Girija

JRF (DST INSPIRE FELLOW)

Center of Innovative and Applied Bioprocessing (CIAB)

(Department of Biotechnology, Government of India)
C-127, 2nd floor, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali
Punjab, India-160071

Mob: +91 7529009198

Email: gir...@ciab.res.in, girija...@gmail.com

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[Francesco Asnicar]

Hi Girija,

The "LM_phylophlan" text file you obtain is the phylogenetic tree in newick format, that's not something related to PhyloPhlAn.

I can suggest different visualization tools that can be used with phylogenetic trees:

• iTOL https://itol.embl.de/
  
• ETE http://etetoolkit.org/
  
• ICYtree https://icytree.org/
  
• Archaeopteryx https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
  
• GraPhlAn https://bitbucket.org/nsegata/graphlan/wiki/Home
  

Many thanks,

Francesco

Email: gir...@ciab.res.in, girija...@gmail.com

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