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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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Python3 version error #14

Closed OluchiAroh closed 3 years ago

OluchiAroh commented 4 years ago

I tried running TEsorter using the python3 version by juke but i keep getting the error below. i installed the anaconda version.

b'\nError: Failed to open binary auxfiles for /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/GyDB2.hmm: use hmmpress first\n\n'.

Any idea how to fix this?

zhangrengang commented 4 years ago

Build the GyDB database firstly:

hmmpress /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/GyDB2.hmm
OluchiAroh commented 4 years ago

I did but i still got the errors.

The first error is Error: failed to open SSI index /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/GyDB2.hmm.h3i

Then followed by b'\nError: Failed to open binary auxfiles for /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/GyDB2.hmm: use hmmpress first\n\n'.

The last error is FileNotFoundError: [Errno 2] No such file or directory: './tmp/chunk_aaseq.1.fasta.domtbl'

The script i ran is

!/bin/bash

module load hmmer/3.1b2

hmmpress /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/GyDB2.hmm

source /opt/asn/etc/asn-bash-profiles-special/modules.sh module load anaconda/3-2020.02

TEsorter genome.final.fa.fasta -db gydb -st nucl -p 20.

Did i place the hmmpress command wrongly?

zhangrengang commented 4 years ago

Look the folder /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/ if hmmpress was sucessful.

OluchiAroh commented 4 years ago

No, it shows this error when i try to hmmpress the file

Error: failed to open SSI index GyDB2.hmm.h3i

zhangrengang commented 4 years ago

Do you have permission to create file in /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/?

OluchiAroh commented 4 years ago

yes i do

zhangrengang commented 4 years ago

You can check the premission by:

touch /mnt/beegfs/apps/dmc/apps/anaconda_3-2020.02/lib/python3.7/site-packages/TEsorter/database/a

I think you should not have the premission.

OluchiAroh commented 4 years ago

Sorry, I don't have permission