I have check my **.fastq.gz file with codes:
# Loop through all .fastq.gz files in the directory
for file in "$input_directory"/*.fastq.gz; do
# Get the first 1000 lines from the file
head -n 1000 "$file" | \
# Extract the quality scores and format as space-separated numbers
awk '{if(NR%4==0) printf("%s",$0);}' | \
# Convert the space-separated numbers to integers
od -A n -t u1 -v | \
# Calculate the minimum and maximum values
awk 'BEGIN{min=100;max=0;} {for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}} \
END {if(max<=74 && min>=33) print "Phred33"; \
else if(max>73 && min<=66) print "Phred64"; \
else if(min>=59 && min<64 && max>73) print "Solexa64"; \
else print "Unknown score encoding";}' \
# Append the result to the output file with the file name
>> "$output_file"
done
and the result is phred64, but when I use command:
time qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path my_manifest.tsv \
--output-path paired-end-demux.qza \
--input-format PairedEndFastqManifestPhred64V2
It comes: File.....File....File ".../qiime2-2023.2/lib/python3.8/site-packages/skbio/io/format/_base.py", line 34, in _decode_qual_to_phred
raise ValueError("Decoded Phred score is out of range [%d, %d]."
ValueError: Decoded Phred score is out of range [0, 62].
An unexpected error has occurred:
Decoded Phred score is out of range [0, 62].
See above for debug info.
I don't know what's going on