TreeShrink error

[sjfleck]

I ran 3 PASTA commands, only 2 of which were successful:

1. PASTA with default parameters (SUCCESS)
   run_pasta.py -d PROTEIN -i protein_sequences.txt -o pasta_job

2. PASTA with RaxML (SUCCESS)
   run_pasta.py -d PROTEIN --raxml-search-after -i protein_sequences.txt -o pasta_job

3. PASTA with RaxML & treeshrink (FAILURE)
   run_pasta.py -d PROTEIN --raxml-search-after --treeshrink-filter -i protein_sequences.txt -o pasta_job

I'm not sure why it failed exactly. these seem to be the relevant lines, but I'll include the entire failure message in my command line:

python: can't open file '/Users/albertlab/pasta-code/pasta/bin/tree_shrink/treeshrink.py': [Errno 2] No such file or directory
cp: input_treeshrink/input_shrunk_0.05.tre: No such file or directory
python: can't open file '/Users/albertlab/pasta-code/pasta/bin/utils/sample_from_subtree.py': [Errno 2] No such file or directory

Any help would be appreciated. Thank you!

NMT_RaxML_treeshrink_filter_error.txt

[smirarab]

Can you confirm the version of the PASTA you have? Do you also mind installing the latest version (including all steps), and running from scratch? I also wonder if you do or do not have /Users/albertlab/pasta-code/pasta/bin/tree_shrink/ after you install the latest version?

…

On Sun, Apr 26, 2020 at 1:58 PM sjfleck ***@***.***> wrote: I ran 3 PASTA commands, only 2 of which were successful: 1. PASTA with default parameters (SUCCESS) *run_pasta.py -d PROTEIN -i protein_sequences.txt -o pasta_job* 2. PASTA with RaxML (SUCCESS) *run_pasta.py -d PROTEIN --raxml-search-after -i protein_sequences.txt -o pasta_job* 3. PASTA with RaxML & treeshrink (FAILURE) *run_pasta.py -d PROTEIN --raxml-search-after --treeshrink-filter -i protein_sequences.txt -o pasta_job* I'm not sure why it failed exactly. these seem to be the relevant lines, but I'll include the entire failure message in my command line: *python: can't open file '/Users/albertlab/pasta-code/pasta/bin/tree_shrink/treeshrink.py': [Errno 2] No such file or directory cp: input_treeshrink/input_shrunk_0.05.tre: No such file or directory python: can't open file '/Users/albertlab/pasta-code/pasta/bin/utils/sample_from_subtree.py': [Errno 2] No such file or directory* Any help would be appreciated. Thank you! NMT_RaxML_treeshrink_filter_error.txt <https://github.com/smirarab/pasta/files/4536461/NMT_RaxML_treeshrink_filter_error.txt> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#50>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXOFWIHNJDDLFHSXO6LTROSOAVANCNFSM4MRMZ4GA> .

-- Siavash Mirarab

[sjfleck]

I believe that I should have the latest version. I followed the installation steps in the readme and on the github page. I used:

git clone https://github.com/smirarab/pasta.git

Would this have not downloaded the newest version? I also checked and I do not have a treeshrink directory in /Users/albertlab/pasta-code/pasta/bin/. I do have a treeshrink executable.

This executable is strange because it's also looking for /tree_shrink/treeshrink.py in its code and when I run it in terminal, I get this:

python: can't open file '/Users/albertlab/pasta-code/pasta/bin/tree_shrink/treeshrink.py': [Errno 2] No such file or directory
cp: input_treeshrink/input_shrunk_0.05.tre: No such file or directory
python: can't open file '/Users/albertlab/pasta-code/pasta/bin/utils/sample_from_subtree.py': [Errno 2] No such file or directory

Maybe I'll try downloading PASTA manually instead of using the git clone command.

[smirarab]

Uyen, does this ring a bell? Any idea what may be going wrong?

…

On Tue, Apr 28, 2020 at 9:19 AM sjfleck ***@***.***> wrote: I believe that I should have the latest version. I followed the installation steps in the readme and on the github page. I used: *git clone https://github.com/smirarab/pasta.git <https://github.com/smirarab/pasta.git>* Would this have not downloaded the newest version? I also checked and I do not have a treeshrink directory in */Users/albertlab/pasta-code/pasta/bin/*. I do have a treeshrink executable. This executable is strange because it's also looking for */tree_shrink/treeshrink.py* in its code and when I run it in terminal, I get this: *python: can't open file '/Users/albertlab/pasta-code/pasta/bin/tree_shrink/treeshrink.py': [Errno 2] No such file or directory cp: input_treeshrink/input_shrunk_0.05.tre: No such file or directory python: can't open file '/Users/albertlab/pasta-code/pasta/bin/utils/sample_from_subtree.py': [Errno 2] No such file or directory* Maybe I'll try downloading PASTA manually instead of using the git clone command. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXODQJCM3QH4AESU4VC3RO36XZANCNFSM4MRMZ4GA> .

-- Siavash Mirarab

[sjfleck]

Hi,
I'm just checking in about this error. If it helps I can share my exact installation steps:

0. I made sure that I had DendroPy (your link is broken, so I followed the installation instructions on https://github.com/jeetsukumaran/DendroPy)
1. mkdir ~/pasta-code
2. cd ~/pasta-code
3. git clone https://github.com/smirarab/pasta.git
4. git clone https://github.com/smirarab/sate-tools-mac.git
5. cd sate-tools-mac
6. git clone https://github.com/koditaraszka/pasta-databases
7. cd ..
8. sudo python setup.py develop
9. added "export CONTRALIGN_DIR=/Users/albertlab/pasta-code/sate-tools-mac" to my ~/.bashrc file

I also can't find "bin/tree_shrink/treeshrink.py" within the files on the code tab on this page. What you have on the code tab matches pretty well with what is on my computer locally. We both seem to have a "treeshrink" in our bin directory, but not a directory named "tree_shrink" or the "treeshrink.py" file. Is there a step that I'm skipping that generates that directory and .py file?

I also want to mention that PASTA on default settings works, I've been able to make a number of protein trees without any errors. I also, used the test files successfully, except in two cases, both of which are in step 6 of the pasta-tutorial.md in the "pasta-doc" directory:

run_seqtools.py -infile pastajob_temp_iteration_0_seq_alignment.txt -outfile iter0.phylip -informat COMPACT3 -outformat PHYLIP -masksites 5 -rename pastajob_temp_name_translation.txt

• I get an error here saying that the infile isn't COMPACT3

run_seqtools.py -infile pastajob.marker001.small.aln -informat FASTA -outfile pata-masked-20.fasta -outformat FASTA -maskmin 20

• i get an error here saying that -maskmin isn't in the usage of run_seqtools.py

I'm not sure why I'm having these issues, but any help would be appreciated

[smirarab]

Sorry for the delay. We will get to this hopefully early next week.

…

On Sun, May 24, 2020 at 10:27 AM sjfleck ***@***.***> wrote: Hi, I'm just checking in about this error. If it helps I can share my exact installation steps: 1. I made sure that I had DendroPy (your link is broken, so I followed the installation instructions on https://github.com/jeetsukumaran/DendroPy) 2. mkdir ~/pasta-code 3. cd ~/pasta-code 4. git clone https://github.com/smirarab/pasta.git 5. git clone https://github.com/smirarab/sate-tools-mac.git 6. cd sate-tools-mac 7. git clone https://github.com/koditaraszka/pasta-databases 8. cd .. 9. sudo python setup.py develop 10. added "export CONTRALIGN_DIR=/Users/albertlab/pasta-code/sate-tools-mac" to my ~/.bashrc file I also can't find "bin/tree_shrink/treeshrink.py" within the files on the code tab on this page. What you have on the code tab matches pretty well with what is on my computer locally. We both seem to have a "treeshrink" in our bin directory, but not a directory named "tree_shrink" or the "treeshrink.py" file. Is there a step that I'm skipping that generates that directory and .py file? I also want to mention that PASTA on default settings works, I've been able to make a number of protein trees without any errors. I also, used the test files successfully, except in two cases, both of which are in step 6 of the pasta-tutorial.md in the "pasta-doc" directory: run_seqtools.py -infile pastajob_temp_iteration_0_seq_alignment.txt -outfile iter0.phylip -informat COMPACT3 -outformat PHYLIP -masksites 5 -rename pastajob_temp_name_translation.txt - I get an error here saying that the infile isn't COMPACT3 run_seqtools.py -infile pastajob.marker001.small.aln -informat FASTA -outfile pata-masked-20.fasta -outformat FASTA -maskmin 20 - i get an error here saying that -maskmin isn't in the usage of run_seqtools.py I'm not sure why I'm having these issues, but any help would be appreciated — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXOADAIG3HAGY6SBSMH3RTFKH5ANCNFSM4MRMZ4GA> .

-- Siavash Mirarab

[RobBarringer]

Hi Siavash and sjfleck,

I'm getting the same error, and I might have spotted something but I'm not too sure. Below is the error returned by my system that seems identical to sjflecks:

And when I look in the pasta/bin directory, I find that treeshrink is a standalone file and isn't in it's own directory, which the error file seems to be searching for (in /bin/tree_shrink/treeshrink.py instead of /bin/treeshrink):

Not sure if it's just a simple problem of the program searching for treeshrink in the wrong directory, but I thought I'd highlight it.

Seems to work perfectly when treeshrink isn't used though!

Thanks a lot,

Rob Barringer

[smirarab]

Hi All, It seems we had intended to remove TreeShrink from within PASTA but we had failed to remove the option. Let me investigate further and either add it back or remove it completely. In the meantime, you can use TreeShrink on the output of PASTA: https://github.com/uym2/TreeShrink Please also let me know if you have a specific use case that would need the integration of TreeShrink within PASTA (as opposed to stand-alone). Thanks Siavash

…

On Mon, Jun 1, 2020 at 8:26 AM RobBarringer ***@***.***> wrote: Hi Siavash and sjfleck, I'm getting the same error, and I might have spotted something but I'm not too sure. Below is the error returned by my system that seems identical to sjflecks: [image: treeshrink_error] <https://user-images.githubusercontent.com/66264345/83424571-7c55d800-a424-11ea-94b2-5b7e067d59eb.png> And when I look in the pasta/bin directory, I find that treeshrink is a standalone file and isn't in it's own directory, which the error file seems to be searching for (in /bin/tree_shrink/treeshrink.py instead of /bin/treeshrink): [image: treeshrink_location] <https://user-images.githubusercontent.com/66264345/83424611-88419a00-a424-11ea-864b-5c16dfca537b.png> Not sure if it's just a simple problem of the program searching for treeshrink in the wrong directory, but I thought I'd highlight it. Seems to work perfectly when treeshrink isn't used though! Thanks a lot, Rob Barringer — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXODWDHFD26UKFQGY3PTRUPCCHANCNFSM4MRMZ4GA> .

-- Siavash Mirarab

[RobBarringer]

Hi All, It seems we had intended to remove TreeShrink from within PASTA but we had failed to remove the option. Let me investigate further and either add it back or remove it completely. In the meantime, you can use TreeShrink on the output of PASTA: https://github.com/uym2/TreeShrink Please also let me know if you have a specific use case that would need the integration of TreeShrink within PASTA (as opposed to stand-alone). Thanks Siavash
…

Hi Siavash,

OK great, thanks for clarifying!

Cheers,

Rob