When I ran the 9th step of the pipeline, the entire log file showed no error messages. However, the final result indicated: 0 reads were mapped with DIAMOND and Sequences mapped to 0 proteins. Could you assist me in resolving this issue? Below, I have provided the log file and the code used for the operation.
code:
!/bin/bash
INPATH='../DF-1-CP20m1'
OUTPATH='..DF-1-CP20m1'
INDEX_PATH="../index_02"
mkdir -p $INDEX_PATH
echo "Index path created: $INDEX_PATH"
cp ../microbial_all_cds.fasta $INDEX_PATH/microbial_all_cds.fasta
bwa index -a bwtsw $INDEX_PATH/microbial_all_cds.fasta
samtools faidx $INDEX_PATH/microbial_all_cds.fasta
Hi,
When I ran the 9th step of the pipeline, the entire log file showed no error messages. However, the final result indicated: 0 reads were mapped with DIAMOND and Sequences mapped to 0 proteins. Could you assist me in resolving this issue? Below, I have provided the log file and the code used for the operation. code:
!/bin/bash
INPATH='../DF-1-CP20m1' OUTPATH='..DF-1-CP20m1'
INDEX_PATH="../index_02" mkdir -p $INDEX_PATH
echo "Index path created: $INDEX_PATH"
cp ../microbial_all_cds.fasta $INDEX_PATH/microbial_all_cds.fasta bwa index -a bwtsw $INDEX_PATH/microbial_all_cds.fasta samtools faidx $INDEX_PATH/microbial_all_cds.fasta
diamond makedb - nr.dmnd
diamond makedb -p 8 --in ../nr/nr.fasta -d $INDEX_PATH/nr.dmnd
BWA
bwa mem -t 4 $INDEX_PATH/microbial_all_cds.fasta $INPATH/CP20m1_contigs.fasta > $OUTPATH/step9/CP20m1_contigs_annotation_bwa.sam bwa mem -t 4 $INDEX_PATH/microbial_all_cds.fasta $INPATH/CP20m1_unassembled.fasta > $OUTPATH/step9/CP20m1_unassembled_annotation_bwa.sam
6_BWA_Gene_Map.py
python3 ../6_BWA_Gene_Map.py \ $INDEX_PATH/microbial_all_cds.fasta \ $INPATH/CP20m1_contigs_map.tsv \ $OUTPATH/step9/CP20m1_genes_map.tsv \ $OUTPATH/step9/CP20m1_genes.fasta \ $INPATH/CP20m1_contigs.fasta \ $OUTPATH/step9/CP20m1_contigs_annotation_bwa.sam \ $OUTPATH/step9/CP20m1_contigs_unmapped.fasta \ $INPATH/CP20m1_unassembled.fastq \ $OUTPATH/step9/CP20m1_unassembled_annotation_bwa.sam \ $OUTPATH/step9/CP20m1_unassembled_unmapped.fasta
DIAMOND against the non-redundant (NR) protein DB
mkdir -p $OUTPATH/step9/dmnd_tmp
diamond blastx
diamond blastx -p 4 -d $INDEX_PATH/nr.dmnd -q $OUTPATH/step9/CP20m1_contigs_unmapped.fasta -o $OUTPATH/step9/CP20m1_contigs.dmdout -f 6 -t $OUTPATH/step9/dmnd_tmp -k 10 --id 85 --query-cover 65 --min-score 60 diamond blastx -p 4 -d $INDEX_PATH/nr.dmnd -q $OUTPATH/step9/CP20m1_unassembled_unmapped.fasta -o $OUTPATH/step9/CP20m1_unassembled.dmdout -f 6 -t $OUTPATH/step9/dmnd_tmp -k 10 --id 85 --query-cover 65 --min-score 60
7_Diamond_Protein_Map.py
python3 /home/xulab_ppg/gaolus_transcript/7_Diamond_Protein_Map.py \ /home/xulab_ppg/nr/nr.fasta \ $INPATH/CP20m1_contigs_map.tsv \ $OUTPATH/step9/CP20m1_genes_map.tsv \ $OUTPATH/step9/CP20m1_proteins.fasta \ $OUTPATH/step9/CP20m1_contigs_unmapped.fasta \ $OUTPATH/step9/CP20m1_contigs.dmdout \ $OUTPATH/step9/CP20m1_contigs_unannotated.fasta \ $OUTPATH/step9/CP20m1_unassembled_unmapped.fasta \ $OUTPATH/step9/CP20m1_unassembled.dmdout \ $OUTPATH/step9/CP20m1_unassembled_unannotated.fasta
rm -r $INDEX_PATHL
Log file: Annottate.log