AttributeError: 'str' object has no attribute 'decode'. Did you mean: 'encode'?

[mooreld]

Hello,

I am using a Linux OS on a University cluster and I am running phyluce/1.7.3-foss-2023a

I am trying to find UCE loci in a single genome using the following code:

#!/bin/bash
#SBATCH --job-name=2bit_scan
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --mem=100gb
#SBATCH --time=72:00:00

phyluce_probe_run_multiple_lastzs_sqlite --db CampRap.sqlite --output CampRap-genome-lastz --scaffoldlist CampRap --genome-base-path ./ --probefile hymenoptera-v2-PRINCIPAL-bait.fasta --cores 12

but I keep getting the same error at the end:

AttributeError: 'str' object has no attribute 'decode'. Did you mean: 'encode'?

I then followed the tutorial Tutorial III: Harvesting UCE Loci From Genomes using the following code:

#!/bin/bash
#SBATCH --job-name=2bit_scan
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --mem=100gb
#SBATCH --time=72:00:00

phyluce_probe_run_multiple_lastzs_sqlite --db tutorial3.sqlite --output tutorial3-genome-lastz --scaffoldlist galGal4 allMis1 --genome-base-path ./ --probefile uce-5k-probes.fasta --cores 12

# I use allMis1 because I downloaded an Alligator mississippiensis genome directly from 'UCSC Genome Browser' rather than NCBI like you do in the tutorial and I believe that should be the only difference between my run and your tutorial.

and I still get the same error.

Here is the full report for the tutorial run:

2025-04-01 13:35:44,506 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - ======= Starting phyluce_probe_run_multiple_lastzs_sqlite =======
2025-04-01 13:35:44,506 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Version: 1.7.3
2025-04-01 13:35:44,506 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Commit: None
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --append: False
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --base_path: ./
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --chromolist: []
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --cores: 12
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --coverage: 83.0
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --db: /scratch/ldm95149/phyluce/uce-genome-tutorial/tutorial3.sqlite
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --identity: 92.5
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --log_path: None
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --no_dir: False
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --output: /scratch/ldm95149/phyluce/uce-genome-tutorial/tutorial3-genome-lastz
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --probefile: /scratch/ldm95149/phyluce/uce-genome-tutorial/uce-5k-probes.fasta
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --scaffoldlist: ['galGal4', 'allMis1']
2025-04-01 13:35:44,507 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Argument --verbosity: INFO
2025-04-01 13:35:44,510 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Checking to ensure all genome sequences exist as 2bit files
2025-04-01 13:35:44,512 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Created species table
2025-04-01 13:35:44,669 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Aligning against galGal4 scaffolds
2025-04-01 13:35:44,704 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Running against galGal4.2bit
2025-04-01 13:35:44,704 - phyluce_probe_run_multiple_lastzs_sqlite - INFO - Running with the --huge option. Chunking files into 10000000 bp...
Traceback (most recent call last):
File "/apps/eb/phyluce/1.7.3-foss-2023a/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 297, in
main()
File "/apps/eb/phyluce/1.7.3-foss-2023a/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 286, in main
align_against_scaffolds(log, cur, args, path)
File "/apps/eb/phyluce/1.7.3-foss-2023a/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 211, in align_against_scaffolds
multi_lastz_runner(
File "/apps/eb/phyluce/1.7.3-foss-2023a/lib/python3.11/site-packages/phyluce/many_lastz.py", line 135, in multi_lastz_runner
chromos = chunk_scaffolds(log, target, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/eb/phyluce/1.7.3-foss-2023a/lib/python3.11/site-packages/phyluce/many_lastz.py", line 94, in chunk_scaffolds
">{0}\n{1}\n".format(seq.decode("utf-8"), sequence)
^^^^^^^^^^
AttributeError: 'str' object has no attribute 'decode'. Did you mean: 'encode'?

In the Traceback, the carets were originally pointing to "chunk_scaffolds(log, target, size)" and "seq.decode".

Is this perhaps an issue with how Phyluce was installed?

I appreciate any help you can offer!

[brantfaircloth]

Howdy,

It looks like you are running python 3.11 but phyluce expects python 3.6. I think the error arises because the .decode() method was removed from python3 at some point btw. v3.6 and 3.11 (but I don't know exactly when). You can try and remove this and other uses of .decode() - e.g. edit the code here to something like:

            temp_out_handle.write(
                ">{0}\n{1}\n".format(seq, sequence)
            )

But I'm also not entirely sure what will happen because I have not tested this. The other alternative is to install phyluce in the python 3.6 environment that is expected by following the installation instructions - that approach seems to work fine for me (I just ran the galGal4 example from the tutorial).

[mooreld]

Thank you for the help! I'm talking with university IT and we are going to try your first suggestion of removing .decode(). I will update if it works or not.