Open brchn6 opened 3 months ago
Script Calling:
# Define input and output files
FASTA_DATA_FILE=/home/projects/zeevid/Analyses/2023-VernalPool/2024-Bar_Cohen_analysis/Done_Results/post_Cleannig_Contis_From_low_Q_conting/output_dir_clean_contigs_length_threshold_coverage_threshold/cleaned_contigs.fasta
OUTPUT_DIR=/home/projects/zeevid/Analyses/2023-VernalPool/2024-Bar_Cohen_analysis/eggNOG-mapper_with_diamond_and_prodigal
OUTPUT_DIR_TMP=${OUTPUT_DIR}/tmp
OUTPUT_FILE_PREFIX=${OUTPUT_DIR}/cleaned_contigs_annotation
HITS_FILE=${OUTPUT_FILE_PREFIX}/hits.tsv
# Ensure output directory and file paths are correct
mkdir -p $OUTPUT_DIR_TMP
chmod -R 755 $OUTPUT_DIR_TMP
# Check if the source and destination files are the same
if [ "$FASTA_DATA_FILE" != "$OUTPUT_FILE_PREFIX.fasta" ]; then
echo "Source and destination files are different. Running emapper.py."
# Run eggNOG-mapper
emapper.py \
-i $FASTA_DATA_FILE \
--output_dir $OUTPUT_DIR \
--output $OUTPUT_FILE_PREFIX \
-m diamond \
--cpu 4 \
--itype genome \
--genepred prodigal \
--scratch_dir $OUTPUT_DIR_TMP \
--temp_dir $OUTPUT_DIR_TMP \
--override
Dear @brchn6 ,
Thank you for reporting this. I will label it as a bug, and hopefully we can fix it soon.
Best, Carlos
I've encountered an issue with the wrap_up method in the emapper.py script, where the script throws a shutil.SameFileError when the source and destination paths for copying a file are the same. This error interrupts the execution of the script, preventing it from completing the annotation process.
Steps to Reproduce:
Run the emapper.py script with input parameters that result in the source and destination paths being the same. Observe the shutil.SameFileError in the traceback.
Error Traceback:
Environment: