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smirarab / pasta

PASTA (Practical Alignment using SATe and Transitivity)
GNU General Public License v3.0
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Docker not working with MUSCLE aligner #56

Closed A-Swafford closed 7 months ago

A-Swafford commented 4 years ago

Installed Docker, image installs fine, help and --exportconfig work fine, runs fine under mafft. Switched the config "aligner =" option to "muscle" and get this error: 

Unknown option "build_mst" in section "sate" skipped!
PASTA INFO: Reading input sequences from 'tub_dataset_20201028.fasta'...
Unknown option "build_mst" in section "sate" skipped!
PASTA INFO: Configuration written to "/data/pasta_20201028_temp_pasta_config.txt".

PASTA INFO: Directory for temporary files created at /root/.pasta/pasta_20201028/tempu9vyd0wa
PASTA INFO: Name translation information saved to /data/pasta_20201028_temp_name_translation.txt as safe name, original name, blank line format.
PASTA INFO: Creating a starting tree for the PASTA algorithm...
PASTA INFO: Performing initial alignment of the entire data matrix...
PASTA failed because one of the programs it tried to run failed.
The invocation that failed was:
    "/pasta/bin/muscle" "-in" "/root/.pasta/pasta_20201028/tempu9vyd0wa/init_aln/tempmuscle5mq7qqat/input.fasta" "-out" "/root/.pasta/pasta_20201028/tempu9vyd0wa/init_aln/tempmuscle5mq7qqat/input.aligned" "-quiet"

Any help would be appreciated!

smirarab commented 4 years ago

I'll investigate.

On Wed, Oct 28, 2020 at 9:16 AM Andrew Swafford notifications@github.com wrote:

Installed Docker, image installs fine, help and --exportconfig work fine, runs fine under mafft. Switched the config "aligner =" option to "muscle" and get this error:

Unknown option "build_mst" in section "sate" skipped! PASTA INFO: Reading input sequences from 'tub_dataset_20201028.fasta'... Unknown option "build_mst" in section "sate" skipped! PASTA INFO: Configuration written to "/data/pasta_20201028_temp_pasta_config.txt".

PASTA INFO: Directory for temporary files created at /root/.pasta/pasta_20201028/tempu9vyd0wa PASTA INFO: Name translation information saved to /data/pasta_20201028_temp_name_translation.txt as safe name, original name, blank line format. PASTA INFO: Creating a starting tree for the PASTA algorithm... PASTA INFO: Performing initial alignment of the entire data matrix... PASTA failed because one of the programs it tried to run failed. The invocation that failed was: "/pasta/bin/muscle" "-in" "/root/.pasta/pasta_20201028/tempu9vyd0wa/init_aln/tempmuscle5mq7qqat/input.fasta" "-out" "/root/.pasta/pasta_20201028/tempu9vyd0wa/init_aln/tempmuscle5mq7qqat/input.aligned" "-quiet"

Any help would be appreciated!

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-- Siavash Mirarab

smirarab commented 4 years ago

I do not seem to be able to reproduce. I just pulled the docker image, and ran:

docker run -v pwd/data:/data smirarab/pasta run_pasta.py -i small.unaligned.fasta —aligner=muscle

which worked with no issues. If you feel comfortable, please send me the your file (outside git) and I can investigate further.

Also, make sure you have the latest versiof the imaged pulled.

(base) bash-3.2$ docker run -v pwd/data:/data smirarab/pasta run_pasta.py --version PASTA v1.8.5 (base) bash-3.2$ docker images|grep pasta smirarab/pasta latest c48054b1c1b1 7 months ago 1.01GB

On Tue, Nov 3, 2020 at 2:38 PM siavash mirarab smirarab@gmail.com wrote:

I'll investigate.

On Wed, Oct 28, 2020 at 9:16 AM Andrew Swafford notifications@github.com wrote:

Installed Docker, image installs fine, help and --exportconfig work fine, runs fine under mafft. Switched the config "aligner =" option to "muscle" and get this error:

Unknown option "build_mst" in section "sate" skipped! PASTA INFO: Reading input sequences from 'tub_dataset_20201028.fasta'... Unknown option "build_mst" in section "sate" skipped! PASTA INFO: Configuration written to "/data/pasta_20201028_temp_pasta_config.txt".

PASTA INFO: Directory for temporary files created at /root/.pasta/pasta_20201028/tempu9vyd0wa PASTA INFO: Name translation information saved to /data/pasta_20201028_temp_name_translation.txt as safe name, original name, blank line format. PASTA INFO: Creating a starting tree for the PASTA algorithm... PASTA INFO: Performing initial alignment of the entire data matrix... PASTA failed because one of the programs it tried to run failed. The invocation that failed was: "/pasta/bin/muscle" "-in" "/root/.pasta/pasta_20201028/tempu9vyd0wa/init_aln/tempmuscle5mq7qqat/input.fasta" "-out" "/root/.pasta/pasta_20201028/tempu9vyd0wa/init_aln/tempmuscle5mq7qqat/input.aligned" "-quiet"

Any help would be appreciated!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/smirarab/pasta/issues/56, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGJXOFMMKKDKLJKLJSHVNLSNA7XJANCNFSM4TCROU7Q .

-- Siavash Mirarab

-- Siavash Mirarab