option value is invalid: --thread=-Q usage: fastp [options] ... options: -i, --in1 read1 input file name (string [=]) -o, --out1 read1 output file name (string [=]) -I, --in2 read2 input file name (string [=]) -O, --out2 read2 output file name (string [=]) --unpaired1 for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. (string [=]) --unpaired2 for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --umpaired1 (default mode), both unpaired reads will be written to this same file. (string [=]) --failed_out specify the file to store reads that cannot pass the filters. (string [=]) -m, --merge for paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default. --merged_out in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output (string [=]) --include_unmerged in the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default. -6, --phred64 indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33) -z, --compression compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4. (int [=4]) --stdin input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add --interleaved_in. --stdout stream passing-filters reads to STDOUT. This option will result in interleaved FASTQ output for paired-end output. Disabled by default. --interleaved_in indicate that is an interleaved FASTQ which contains both read1 and read2. Disabled by default. --reads_to_process specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0]) --dont_overwrite don't overwrite existing files. Overwritting is allowed by default. -V, --verbose output verbose log information (i.e. when every 1M reads are processed). -A, --disable_adapter_trimming adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled -a, --adapter_sequence the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto]) --adapter_sequence_r2 the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as (string [=auto]) --adapter_fasta specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file (string [=]) --detect_adapter_for_pe by default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data. -f, --trim_front1 trimming how many bases in front for read1, default is 0 (int [=0]) -t, --trim_tail1 trimming how many bases in tail for read1, default is 0 (int [=0]) -b, --max_len1 if read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1. Default 0 means no limitation (int [=0]) -F, --trim_front2 trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0]) -T, --trim_tail2 trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0]) -B, --max_len2 if read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2. Default 0 means no limitation. If it's not specified, it will follow read1's settings (int [=0]) -g, --trim_poly_g force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data --poly_g_min_len the minimum length to detect polyG in the read tail. 10 by default. (int [=10]) -G, --disable_trim_poly_g disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data -x, --trim_poly_x enable polyX trimming in 3' ends. --poly_x_min_len the minimum length to detect polyX in the read tail. 10 by default. (int [=10]) -5, --cut_front move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise. -3, --cut_tail move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise. -r, --cut_right move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop. -W, --cut_window_size the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4]) -M, --cut_mean_quality the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int [=20]) --cut_front_window_size the window size option of cut_front, default to cut_window_size if not specified (int [=4]) --cut_front_mean_quality the mean quality requirement option for cut_front, default to cut_mean_quality if not specified (int [=20]) --cut_tail_window_size the window size option of cut_tail, default to cut_window_size if not specified (int [=4]) --cut_tail_mean_quality the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified (int [=20]) --cut_right_window_size the window size option of cut_right, default to cut_window_size if not specified (int [=4]) --cut_right_mean_quality the mean quality requirement option for cut_right, default to cut_mean_quality if not specified (int [=20]) -Q, --disable_quality_filtering quality filtering is enabled by default. If this option is specified, quality filtering is disabled -q, --qualified_quality_phred the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15]) -u, --unqualified_percent_limit how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40]) -n, --n_base_limit if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5]) -e, --average_qual if one read's average quality score =1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0]) -d, --split_prefix_digits the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4]) --cut_by_quality5 DEPRECATED, use --cut_front instead. --cut_by_quality3 DEPRECATED, use --cut_tail instead. --cut_by_quality_aggressive DEPRECATED, use --cut_right instead. --discard_unmerged DEPRECATED, no effect now, see the introduction for merging. -?, --help print this message