swarris / pyPaSWAS

Program for DNA/RNA/protein sequence alignment, read mapping and trimming. Extended python version of PaSWAS, supporting OpenCL and CUDA devices.
MIT License
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Warning: No Suitable hits produced #12

Closed lixx21 closed 11 months ago

lixx21 commented 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

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...
swarris commented 11 months ago

Hi! You need to provide the file format for the second file as well: -2 fastq