Closed lixx21 closed 11 months ago
Hi, I am trying to run this with this command: python pypaswas.py fasta1.fastq fasta1.fastq -1 fastq -o out.txt --loglevel=DEBUG
python pypaswas.py fasta1.fastq fasta1.fastq -1 fastq -o out.txt --loglevel=DEBUG
and I just got this debug. what it means by that warning?
INFO - Initializing application... DEBUG - Initializing Score... DEBUG - Initializing score finished. DEBUG - Initializing DnaRnaScore... DEBUG - Creating matrix with parameters: match_score: 5, mismatch_score: -3, gap_score: -5.0, other_score: -1, any_score: 0 DEBUG - Initializing DnaRnaScore finished. INFO - Application initialized. INFO - Setting program... DEBUG - Initializing aligner... DEBUG - Initializing hitlist... DEBUG - Initializing hitlist OK. DEBUG - Setting SW... DEBUG - Using CUDA implementation DEBUG - Initializing SmithWaterman. INFO - No gap extension penalty detected: using original PaSWAS scoring algorithm DEBUG - Going to initialize device... with number 0 DEBUG - Initializing device 0 DEBUG - Aligner initialized. INFO - Program set. DEBUG - Initializing hitlist... DEBUG - Initializing hitlist OK. INFO - Reading query sequences 0 1000000... DEBUG - Initializing reader path = C:\Users\ASUS\Desktop\pyPaSWAS\fasta1.fastq limitlength = 100000... DEBUG - Initializing reader finished. DEBUG - Reading from fastq file... DEBUG - 1 sequences read. DEBUG - Sorting records on length... INFO - Query sequences OK. INFO - Reading target sequences 0, 100000000... DEBUG - Initializing reader path = C:\Users\ASUS\Desktop\pyPaSWAS\fasta1.fastq limitlength = 100000... DEBUG - Initializing reader finished. DEBUG - Reading from fasta file... INFO - Processing done INFO - Reading query sequences 1000000 2000000... DEBUG - Initializing reader path = C:\Users\ASUS\Desktop\pyPaSWAS\fasta1.fastq limitlength = 100000... DEBUG - Initializing reader finished. DEBUG - Reading from fastq file... INFO - Processing OK (0 hits found). WARNING - No suitable hits produced, exiting...
Hi! You need to provide the file format for the second file as well: -2 fastq
Hi, I am trying to run this with this command:
python pypaswas.py fasta1.fastq fasta1.fastq -1 fastq -o out.txt --loglevel=DEBUG
and I just got this debug. what it means by that warning?