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osuchanglab / autoMLSA

Automated Multi-Locus Sequence Analysis (MLSA) pipeline
GNU General Public License v3.0
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cannot install Bio.SeqIO #1

Open pavlo888 opened 4 years ago

pavlo888 commented 4 years ago

Dear Sir/Madam,

I am really interested in using this pipeline. However, it seems that I cannot install all the dependencies .So far, I have been able to install most of the dependencies in a Conda environment using either "Conda install" or "pip install" commands.

I have also force installed Bio.SeqIO using pip but unfortunately it seems it does not work.

When I try to run the bash script I get the following message:

Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /anaconda2/envs/automlsa/lib/site_perl/5.26.2/darwin-thread-multi-2level /anaconda2/envs/automlsa/lib/site_perl/5.26.2 /anaconda2/envs/automlsa/lib/5.26.2/darwin-thread-multi-2level /anaconda2/envs/automlsa/lib/5.26.2 .) at /Users/pablov/Downloads/autoMLSA-master/autoMLSA.pl line 35. BEGIN failed--compilation aborted at /Users/pablov/Downloads/autoMLSA-master/autoMLSA.pl line 35.

Do you have any idea how can I solve this issue?

Thank you very much in advance.

Best regards, Pablo

davised commented 4 years ago

Hi Pablo,

You'll need the Perl Bio::SeqIO module, which is install using cpan/cpanm. I presume you can install this using conda as well but I haven't done that myself.

The python Bio module SeqIO is what was installed using pip, which isn't what is needed in this case.

Try looking for the Perl Bio module in bioconda and see if you can get it working that way. I'll be able to help more directly on Tuesday if you can't get it working by then.

Thanks,

Ed

On Sat, Nov 9, 2019, 1:46 PM pavlo888 notifications@github.com wrote:

Dear Sir/Madam,

I am really interested in using this pipeline. However, it seems that I cannot install all the dependencies .So far, I have been able to install most of the dependencies in a Conda environment using either "Conda install" or "pip install" commands.

I have also force installed Bio.SeqIO using pip but unfortunately it seems it does not work.

When I try to run the bash script I get the following message:

Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /anaconda2/envs/automlsa/lib/site_perl/5.26.2/darwin-thread-multi-2level /anaconda2/envs/automlsa/lib/site_perl/5.26.2 /anaconda2/envs/automlsa/lib/5.26.2/darwin-thread-multi-2level /anaconda2/envs/automlsa/lib/5.26.2 .) at /Users/pablov/Downloads/autoMLSA-master/autoMLSA.pl line 35. BEGIN failed--compilation aborted at /Users/pablov/Downloads/autoMLSA-master/autoMLSA.pl line 35.

Do you have any idea how can I solve this issue?

Thank you very much in advance.

Best regards, Pablo

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pavlo888 commented 4 years ago

Hi Ed,

Thanks a lot for your reply! I installed the Bio Perl module with the command cpanm Bio::Perl.

However, now I have another problem. It seems that my Entrez package is not working correctly.

When I run the script, I get the following log:

`Generating folder sample_run_agro1 sh: lscpu: command not found Unable to check threads setting. Ensure you have enetered the proper number of threads or performance will be degraded (set to less than # of processors). No alignment program chosen. Setting to use mafft-linsi. Assuming blast executables in PATH Found BLAST version 2.2.31 or greater

Blast searches started at Sun Nov 10 23:15:15 2019

Performing BLAST search for rpoB_WP_065113666.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5

of alignments => 500

of threads => 2

Wrote BLAST results to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.out Performing BLAST search for recA_WP_065115971.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5

of alignments => 500

of threads => 2

Wrote BLAST results to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.out Performing BLAST search for trpD_WP_065115826.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5

of alignments => 500

of threads => 2

Wrote BLAST results to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.out

Finished blast searches at Sun Nov 10 23:15:16 2019.

Extracting sequences from BLAST searches Wrote fasta file to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.fas Wrote fasta file to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.fas Wrote fasta file to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.fas

Finished extracting blast searches at Sun Nov 10 23:15:17 2019.

Finding taxonomic and naming information. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : No such file or directory at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 1. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 2. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 3. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 4. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile. Check your parameters and connection and try again`

Could you help me solve this issue? Thanks!

Cheers, Pablo

davised commented 4 years ago

Hi Pablo,

The eutilities need to either be in your $PATH or the path needs to be supplied in the ./scripts/auto_edirect.pl script.

First run the ./scripts/edirect-dl.pl to download them and then either modify your $PATH as instructed or just add the full path to the edirect download directory to the script listed above.

Good luck,

Ed

On Sun, Nov 10, 2019, 2:21 PM pavlo888 notifications@github.com wrote:

Hi Ed,

Thanks a lot for your reply! I installed the Bio Perl module with the command cpanm Bio::Perl.

However, now I have another problem. It seems that my Entrez package is not working correctly.

When I run the script, I get the following log: `Generating folder sample_run_agro1 sh: lscpu: command not found Unable to check threads setting. Ensure you have enetered the proper number of threads or performance will be degraded (set to less than # of processors). No alignment program chosen. Setting to use mafft-linsi. Assuming blast executables in PATH Found BLAST version 2.2.31 or greater

Blast searches started at Sun Nov 10 23:15:15 2019

Performing BLAST search for rpoB_WP_065113666.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.out Performing BLAST search for recA_WP_065115971.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.out Performing BLAST search for trpD_WP_065115826.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.out

Finished blast searches at Sun Nov 10 23:15:16 2019.

Extracting sequences from BLAST searches Wrote fasta file to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.fas Wrote fasta file to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.fas Wrote fasta file to /Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.fas

Finished extracting blast searches at Sun Nov 10 23:15:17 2019.

Finding taxonomic and naming information. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : No such file or directory at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 1. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 2. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 3. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 4. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile. Check your parameters and connection and try again`

Could you help me solve this issue? Thanks!

Cheers, Pablo

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/osuchanglab/autoMLSA/issues/1?email_source=notifications&email_token=AD4WCP4JRZ5FFPLPIYJ3L7TQTCCP7A5CNFSM4JLJXSXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDVIRBY#issuecomment-552241287, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD4WCP335HE4CEAQOXTKWKLQTCCP7ANCNFSM4JLJXSXA .

pavlo888 commented 4 years ago

Hi Ed,

Thanks a lot for your prompt reply!!! I have successfully installed eutilities. Sorry I oversaw that detail.

However, now I have some other issue... I feel I am getting closer to having the pipeline work

When I run the command: /Users/pablov/Downloads/autoMLSA-master/autoMLSA.pl -email pablo.vargas@kuleuven.be -runid agro_test_run_mlsa -threads 2 -entrez_query 357 -local_db all.fas -- agro_test_markers.faa

Then it all seems to work well until abruptly I get the following message:

Compiling and aligning fasta files started at Thu Nov 14 00:12:36 2019; also trimming if desired

cat: /Users/pablov/Downloads/mlsa_test/agro_test_run_mlsa/trpD_WP_065115826.1_vs_all.fas.local.fas: No such file or directory

Unable to compile blast fasta files. Check permissions and try again.

Do you have any idea what is wrong?

I really appreciate your support. Greatly.

Cheers, Pablo

On Mon, Nov 11, 2019 at 3:31 AM Ed Davis notifications@github.com wrote:

Hi Pablo,

The eutilities need to either be in your $PATH or the path needs to be supplied in the ./scripts/auto_edirect.pl script.

First run the ./scripts/edirect-dl.pl to download them and then either modify your $PATH as instructed or just add the full path to the edirect download directory to the script listed above.

Good luck,

Ed

On Sun, Nov 10, 2019, 2:21 PM pavlo888 notifications@github.com wrote:

Hi Ed,

Thanks a lot for your reply! I installed the Bio Perl module with the command cpanm Bio::Perl.

However, now I have another problem. It seems that my Entrez package is not working correctly.

When I run the script, I get the following log: `Generating folder sample_run_agro1 sh: lscpu: command not found Unable to check threads setting. Ensure you have enetered the proper number of threads or performance will be degraded (set to less than # of processors). No alignment program chosen. Setting to use mafft-linsi. Assuming blast executables in PATH Found BLAST version 2.2.31 or greater

Blast searches started at Sun Nov 10 23:15:15 2019

Performing BLAST search for rpoB_WP_065113666.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.out Performing BLAST search for recA_WP_065115971.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.out Performing BLAST search for trpD_WP_065115826.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.out

Finished blast searches at Sun Nov 10 23:15:16 2019.

Extracting sequences from BLAST searches Wrote fasta file to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.fas Wrote fasta file to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.fas Wrote fasta file to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.fas

Finished extracting blast searches at Sun Nov 10 23:15:17 2019.

Finding taxonomic and naming information. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : No such file or directory at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 1. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 2. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 3. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 4. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile. Check your parameters and connection and try again`

Could you help me solve this issue? Thanks!

Cheers, Pablo

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alexweisberg commented 4 years ago

Hi Pablo,

Could you please post the log file for this run? There should be a file called agro_test_run_mlsa.log in the log folder. That way we can see what may have happened. Thanks!

-Alex

davised commented 4 years ago

Hi Pablo,

I think it may be that your target database file has the name 'all' in it.

Could you try renaming the database and starting the analysis over?

Thanks,

Ed

On Wed, Nov 13, 2019, 3:15 PM pavlo888 notifications@github.com wrote:

Hi Ed,

Thanks a lot for your prompt reply!!! I have successfully installed eutilities. Sorry I oversaw that detail.

However, now I have some other issue... I feel I am getting closer to having the pipeline work

When I run the command: /Users/pablov/Downloads/autoMLSA-master/autoMLSA.pl -email pablo.vargas@kuleuven.be -runid agro_test_run_mlsa -threads 2 -entrez_query 357 -local_db all.fas -- agro_test_markers.faa

Then it all seems to work well until abruptly I get the following message:

Compiling and aligning fasta files started at Thu Nov 14 00:12:36 2019; also trimming if desired

cat:

/Users/pablov/Downloads/mlsa_test/agro_test_run_mlsa/trpD_WP_065115826.1_vs_all.fas.local.fas: No such file or directory

Unable to compile blast fasta files. Check permissions and try again.

Do you have any idea what is wrong?

I really appreciate your support. Greatly.

Cheers, Pablo

On Mon, Nov 11, 2019 at 3:31 AM Ed Davis notifications@github.com wrote:

Hi Pablo,

The eutilities need to either be in your $PATH or the path needs to be supplied in the ./scripts/auto_edirect.pl script.

First run the ./scripts/edirect-dl.pl to download them and then either modify your $PATH as instructed or just add the full path to the edirect download directory to the script listed above.

Good luck,

Ed

On Sun, Nov 10, 2019, 2:21 PM pavlo888 notifications@github.com wrote:

Hi Ed,

Thanks a lot for your reply! I installed the Bio Perl module with the command cpanm Bio::Perl.

However, now I have another problem. It seems that my Entrez package is not working correctly.

When I run the script, I get the following log: `Generating folder sample_run_agro1 sh: lscpu: command not found Unable to check threads setting. Ensure you have enetered the proper number of threads or performance will be degraded (set to less than # of processors). No alignment program chosen. Setting to use mafft-linsi. Assuming blast executables in PATH Found BLAST version 2.2.31 or greater

Blast searches started at Sun Nov 10 23:15:15 2019

Performing BLAST search for rpoB_WP_065113666.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.out

Performing BLAST search for recA_WP_065115971.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.out

Performing BLAST search for trpD_WP_065115826.1 to /Users/pablov/Downloads/mlsa_test/all.fas from file /Users/pablov/Downloads/mlsa_test/agro_test_markers.faa.txt... Using these parameters: Blast program => tblastn e-value cutoff => 1e-5 of alignments => 500 of threads => 2

Wrote BLAST results to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.out

Finished blast searches at Sun Nov 10 23:15:16 2019.

Extracting sequences from BLAST searches Wrote fasta file to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/recA_WP_065115971.1_vs_all.fas.local.fas

Wrote fasta file to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/rpoB_WP_065113666.1_vs_all.fas.local.fas

Wrote fasta file to

/Users/pablov/Downloads/mlsa_test/sample_run_agro1/trpD_WP_065115826.1_vs_all.fas.local.fas

Finished extracting blast searches at Sun Nov 10 23:15:17 2019.

Finding taxonomic and naming information. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : No such file or directory at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 1. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 2. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 3. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile on try 4. Trying again. Submitting 1 ids to epost. sh: epost: command not found Unable to run epost command : at /Users/pablov/Downloads/autoMLSA-master/scripts/auto_edirect.pl line 241. Unable to generate keyfile. Check your parameters and connection and try again`

Could you help me solve this issue? Thanks!

Cheers, Pablo

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pavlo888 commented 4 years ago

Hi Ed,

I restarted my analysis with autoMLSA. However, I am now in a distinct environment. I am currently working on Ubuntu MATE and I am having problems installing the Bio::SeqIO perl library. Do you have any idea how should I proceed? I have tried different ways using conda and suod apt-get but it all fails.

Cheers, Pablo