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carnegie / E2P2

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Error when trying to run E2P2 #17

Open lpereira89 opened 1 month ago

lpereira89 commented 1 month ago

Hello, I am trying to use E2P2 in a plant genome (Alloteropsis semialata). I found some errors when trying to run E2P2 and I am not sure about what the problem is (sorry - my bioinformatics experience is limited). I believe that I modified the config.init file correctly and the path to the input file is correct. I appreciate any advice - thank you in advance!

I paste the log file below:

2024-08-12 15:11:55,165 e2p2 INFO MainProcess Temp folder created at path /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902. 2024-08-12 15:11:55,166 e2p2 WARNING MainProcess Log file /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902/e2p2.1723471902.log exists, will append to it... 2024-08-12 15:11:55,166 e2p2 INFO MainProcess No user provided config.ini is found, attempting to use file at /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/config.ini. 2024-08-12 15:11:55,305 e2p2 INFO MainProcess Missing 'blast_bit_score' in 'BLAST' section in config 2024-08-12 15:11:55,305 e2p2 WARNING MainProcess BLAST Bit score in config missing or type error, using default 0.0. 2024-08-12 15:11:55,369 e2p2 INFO MainProcess New process: BLAST: "blastp -db /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/blast/rpsd.v5.2.ef.fasta -num_threads 4 -query /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -out /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902/blast.AUS1_prot.1723471902.out -outfmt 6" 2024-08-12 15:11:55,369 e2p2 INFO MainProcess New process: DEEPEC: "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902" 2024-08-12 15:11:55,369 e2p2 INFO MainProcess Running all available processes. 2024-08-12 15:11:55,371 e2p2 INFO MainProcess Starting Process "blastp -db /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/blast/rpsd.v5.2.ef.fasta -num_threads 4 -query /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -out /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902/blast.AUS1_prot.1723471902.out -outfmt 6" 2024-08-12 15:11:55,372 e2p2 INFO MainProcess Starting Process "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902" 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "blastp -db /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/blast/rpsd.v5.2.ef.fasta -num_threads 4 -query /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -out /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902/blast.AUS1_prot.1723471902.out -outfmt 6", stdout[0]: No such file or directory 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[0]: Traceback (most recent call last): 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[1]: File "/mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py", line 5, in <module> 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[2]: from deepec.__main__ import main 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[3]: File "/mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec/__main__.py", line 9, in <module> 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[4]: from deepec import utils 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[5]: File "/mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec/utils.py", line 6, in <module> 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[6]: from Bio import SeqIO 2024-08-12 15:11:56,074 e2p2 ERROR MainProcess Process Error "python /mnt/parscratch/users/bo1lpg/gene-cluster/E2P2/deepec/deepec.py -i /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.fa -o /mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902", stdout[7]: ModuleNotFoundError: No module named 'Bio' 2024-08-12 15:11:56,074 e2p2 INFO MainProcess Reading blast output: "/mnt/parscratch/users/bo1lpg/gene-cluster/test/AUS1_prot.1723471902/blast.AUS1_prot.1723471902.out"

bxuecarnegie commented 1 month ago

This seem to be caused by missing Python libraries required to run DeepEC. You can check the forked repo at https://github.com/bxuecarnegie/deepec and the dependencies listed in the environment.yml file.