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[]$ cutadapt --version
2.10

[]$ cutadapt --help
cutadapt version 2.10

Copyright (C) 2010-2020 Marcel Martin <marcel.martin@scilifelab.se>

cutadapt removes adapter sequences from high-throughput sequencing reads.

Usage:
    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

For paired-end reads:
    cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq

Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
characters are supported. All reads from input.fastq will be written to
output.fastq with the adapter sequence removed. Adapter matching is
error-tolerant. Multiple adapter sequences can be given (use further -a
options), but only the best-matching adapter will be removed.

Input may also be in FASTA format. Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.

Citation:

Marcel Martin. Cutadapt removes adapter sequences from high-throughput
sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
http://dx.doi.org/10.14806/ej.17.1.200

Run "cutadapt --help" to see all command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.

Options:
  -h, --help            Show this help message and exit
  --version             Show version number and exit
  --debug [{trace}]     Print debug log. 'trace' prints also DP matrices
  -j CORES, --cores CORES
                        Number of CPU cores to use. Use 0 to auto-detect. Default: 1

Finding adapters:
  Parameters -a, -g, -b specify adapters to be removed from each read (or from the first read in a pair if data is paired). If specified multiple times, only the best
  matching adapter is trimmed (but see the --times option). When the special notation 'file:FILE' is used, adapter sequences are read from the given FASTA file.

  -a ADAPTER, --adapter ADAPTER
                        Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character
                        is appended ('anchoring'), the adapter is only found if it is a suffix of the read.
  -g ADAPTER, --front ADAPTER
                        Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches
                        at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read.
  -b ADAPTER, --anywhere ADAPTER
                        Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under -a und
                        -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for
                        rescuing failed library preparations - do not use if you know which end your adapter was ligated to!
  -e RATE, --error-rate RATE
                        Maximum allowed error rate as value between 0 and 1 (no. of errors divided by length of matching region). Default: 0.1 (=10%)
  --no-indels           Allow only mismatches in alignments. Default: allow both mismatches and indels
  -n COUNT, --times COUNT
                        Remove up to COUNT adapters from each read. Default: 1
  -O MINLENGTH, --overlap MINLENGTH
                        Require MINLENGTH overlap between read and adapter for an adapter to be found. Default: 3
  --match-read-wildcards
                        Interpret IUPAC wildcards in reads. Default: False
  -N, --no-match-adapter-wildcards
                        Do not interpret IUPAC wildcards in adapters.
  --action {trim,mask,lowercase,none}
                        What to do with found adapters. mask: replace with 'N' characters; lowercase: convert to lowercase; none: leave unchanged (useful with --discard-
                        untrimmed). Default: trim
  --rc, --revcomp       Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. Default: check
                        only read

Additional read modifications:
  -u LENGTH, --cut LENGTH
                        Remove bases from each read (first read only if paired). If LENGTH is positive, remove bases from the beginning. If LENGTH is negative, remove
                        bases from the end. Can be used twice if LENGTHs have different signs. This is applied *before* adapter trimming.
  --nextseq-trim 3'CUTOFF
                        NextSeq-specific quality trimming (each read). Trims also dark cycles appearing as high-quality G bases.
  -q [5'CUTOFF,]3'CUTOFF, --quality-cutoff [5'CUTOFF,]3'CUTOFF
                        Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is
                        given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the
                        second.
  --quality-base N      Assume that quality values in FASTQ are encoded as ascii(quality + N). This needs to be set to 64 for some old Illumina FASTQ files. Default: 33
  --length LENGTH, -l LENGTH
                        Shorten reads to LENGTH. Positive values remove bases at the end while negative ones remove bases at the beginning. This and the following
                        modifications are applied after adapter trimming.
  --trim-n              Trim N's on ends of reads.
  --length-tag TAG      Search for TAG followed by a decimal number in the description field of the read. Replace the decimal number with the correct length of the
                        trimmed read. For example, use --length-tag 'length=' to correct fields like 'length=123'.
  --strip-suffix STRIP_SUFFIX
                        Remove this suffix from read names if present. Can be given multiple times.
  -x PREFIX, --prefix PREFIX
                        Add this prefix to read names. Use {name} to insert the name of the matching adapter.
  -y SUFFIX, --suffix SUFFIX
                        Add this suffix to read names; can also include {name}
  --zero-cap, -z        Change negative quality values to zero.

Filtering of processed reads:
  Filters are applied after above read modifications. Paired-end reads are always discarded pairwise (see also --pair-filter).

  -m LEN[:LEN2], --minimum-length LEN[:LEN2]
                        Discard reads shorter than LEN. Default: 0
  -M LEN[:LEN2], --maximum-length LEN[:LEN2]
                        Discard reads longer than LEN. Default: no limit
  --max-n COUNT         Discard reads with more than COUNT 'N' bases. If COUNT is a number between 0 and 1, it is interpreted as a fraction of the read length.
  --max-expected-errors ERRORS, --max-ee ERRORS
                        Discard reads whose expected number of errors (computed from quality values) exceeds ERRORS.
  --discard-trimmed, --discard
                        Discard reads that contain an adapter. Use also -O to avoid discarding too many randomly matching reads.
  --discard-untrimmed, --trimmed-only
                        Discard reads that do not contain an adapter.
  --discard-casava      Discard reads that did not pass CASAVA filtering (header has :Y:).

Output:
  --quiet               Print only error messages.
  --report {full,minimal}
                        Which type of report to print: 'full' or 'minimal'. Default: full
  -o FILE, --output FILE
                        Write trimmed reads to FILE. FASTQ or FASTA format is chosen depending on input. Summary report is sent to standard output. Use '{name}' for
                        demultiplexing (see docs). Default: write to standard output
  --fasta               Output FASTA to standard output even on FASTQ input.
  -Z                    Use compression level 1 for gzipped output files (faster, but uses more space)
  --info-file FILE      Write information about each read and its adapter matches into FILE. See the documentation for the file format.
  -r FILE, --rest-file FILE
                        When the adapter matches in the middle of a read, write the rest (after the adapter) to FILE.
  --wildcard-file FILE  When the adapter has N wildcard bases, write adapter bases matching wildcard positions to FILE. (Inaccurate with indels.)
  --too-short-output FILE
                        Write reads that are too short (according to length specified by -m) to FILE. Default: discard reads
  --too-long-output FILE
                        Write reads that are too long (according to length specified by -M) to FILE. Default: discard reads
  --untrimmed-output FILE
                        Write reads that do not contain any adapter to FILE. Default: output to same file as trimmed reads

Paired-end options:
  The -A/-G/-B/-U options work like their -a/-b/-g/-u counterparts, but are applied to the second read in each pair.

  -A ADAPTER            3' adapter to be removed from second read in a pair.
  -G ADAPTER            5' adapter to be removed from second read in a pair.
  -B ADAPTER            5'/3 adapter to be removed from second read in a pair.
  -U LENGTH             Remove LENGTH bases from second read in a pair.
  -p FILE, --paired-output FILE
                        Write second read in a pair to FILE.
  --pair-adapters       Treat adapters given with -a/-A etc. as pairs. Either both or none are removed from each read pair.
  --pair-filter (any|both|first)
                        Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any
  --interleaved         Read and/or write interleaved paired-end reads.
  --untrimmed-paired-output FILE
                        Write second read in a pair to this FILE when no adapter was found. Use with --untrimmed-output. Default: output to same file as trimmed reads
  --too-short-paired-output FILE
                        Write second read in a pair to this file if pair is too short. Use also --too-short-output.
  --too-long-paired-output FILE
                        Write second read in a pair to this file if pair is too long. Use also --too-long-output.

#SBATCH --cpus-per-task=16