I am new with Phyluce and I need your help, please

[luishdez35]

I try to run the tutorial and, in the assemble I obtain this:

(phyluce-1.7.1) luiscarloshernandez@MacBook-Air-de-Luis uce-tutorial % phyluce_assembly_assemblo_spades \ --conf assembly.conf \ --output spades-assemblies \ --cores 2 2021-07-19 18:55:20,842 - phyluce_assembly_assemblo_spades - INFO - =========== Starting phyluce_assembly_assemblo_spades =========== 2021-07-19 18:55:20,843 - phyluce_assembly_assemblo_spades - INFO - Version: 1.7.1 2021-07-19 18:55:20,843 - phyluce_assembly_assemblo_spades - INFO - Commit: None 2021-07-19 18:55:20,843 - phyluce_assembly_assemblo_spades - INFO - Argument --config: /Users/luiscarloshernandez/uce-tutorial/assembly.conf 2021-07-19 18:55:20,843 - phyluce_assembly_assemblo_spades - INFO - Argument --cores: 2 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --dir: None 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --log_path: None 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --memory: 8 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --no_clean: False 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --output: /Users/luiscarloshernandez/uce-tutorial/spades-assemblies 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --subfolder: 2021-07-19 18:55:20,844 - phyluce_assembly_assemblo_spades - INFO - Argument --verbosity: INFO 2021-07-19 18:55:20,845 - phyluce_assembly_assemblo_spades - INFO - Getting input filenames and creating output directories Traceback (most recent call last): File "/Users/luiscarloshernandez/opt/anaconda3/envs/phyluce-1.7.1/lib/python3.6/site-packages/phyluce/raw_reads.py", line 173, in get_input_data os.path.abspath(os.path.expanduser(sample[1])) AssertionError

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Users/luiscarloshernandez/opt/anaconda3/envs/phyluce-1.7.1/bin/phyluce_assembly_assemblo_spades", line 231, in main() File "/Users/luiscarloshernandez/opt/anaconda3/envs/phyluce-1.7.1/bin/phyluce_assembly_assemblo_spades", line 184, in main input_data = get_input_data(args.config, args.dir) File "/Users/luiscarloshernandez/opt/anaconda3/envs/phyluce-1.7.1/lib/python3.6/site-packages/phyluce/raw_reads.py", line 176, in get_input_data raise IOError("{} is not a directory".format(sample[1])) OSError: /Users/luiscarloshernandez/uce-tutorial/uce-tutorial/clean-fastq/anolis_carolinensis/split-adapter-quality-trimmed is not a directory

I hope you can help me please.

[brantfaircloth]

This error is telling you that the folder/directory at /Users/luiscarloshernandez/uce-tutorial/uce-tutorial/clean-fastq/anolis_carolinensis/split-adapter-quality-trimmed does not exist (but the program expects for it to exist and contain clean sequence reads).

[luishdez35]

Thanks a lot for your help, I create de configuration file with this command:

cd clean-fastq
echo "[samples]" > ../assembly.conf
for i in *; \
   do echo $i":/Users/luiscarloshernandez/uce-tutorial/clean-fastq/"$i"/split-adapter-quality-trimmed/"; \
   done >> ../assembly.conf

Then I update conda and all work again.

I have another question Dr. Faircloth, What Macbook or iMac do you recommend for use Phyluce, with the minimum and maximum requirements. I am a PhD student and i'm learning bioinformatics, so i'm new to a lot of things. Thanks a lot

[brantfaircloth]

We usually use machines with at least 48 Gb RAM (these are mostly linux machines or HPC cluster machines). You can get a macbook or imac to work, but you would probably want at least 24 Gb RAM on an imac (and ideally 8-12 compute cores).

[luishdez35]

Thanks a lot for your answer.

Cheers

[NYX-PLUTO]

Hi Professor Faircloth,

I am also very new to bioinformatics.
I get the same error ("OSError: /home/tobyhays/uce-tutorial/clean-fastq/alligator_mississippiensis/split-adapter-quality-trimmed is not a directory") and have tried using the method given above:

echo "[samples]" > ../assembly.conf
for i in *; \
   do echo $i":/home/tobyhays/uce-tutorial/clean-fastq/"$i"/split-adapter-quality trimmed/"; \
   done >> ../assembly.conf

without success. I'm attaching the assembly.conf file I am using as a .txt file. assembly.txt

Thanks for your help and patience.

[brantfaircloth]

Howdy,

Your config file looks ok, but what is the contents of each folder. E.g., what does:

ls -l /home/tobyhays/uce-tutorial/clean-fastq/alligator_mississippiensis/split-adapter-quality-trimmed/

look like? similarly, what does:

ls -l /home/tobyhays/uce-tutorial/clean-fastq/anolis_carolinensis/split-adapter-quality-trimmed/

look like?