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在做16s RNA分析,使用qiime vsearch合并双端序列。以下是我的代码
#!/bin/bash
#PBS -q batch
#PBS -o merge.o
#PBS -e merge.e
source activate qiime2-2022.8
cd /home/libofeng/yangyang990124/16s/trim/
qiime vsearch join-pairs
--i-demultiplexed-seqs reads_trimmed.qza
--o-joined-sequences reads_trimmed_joined.qza
然后报错
Usage: qiime vsearch join-pairs [OPTIONS]
Join paired-end sequence reads using vsearch's merge_pairs function. See the
vsearch documentation for details on how paired-end joining is performed,
and for more information on the parameters to this method.
Inputs:
--i-demultiplexed-seqs ARTIFACT SampleData[PairedEndSequencesWithQuality]
The demultiplexed paired-end sequences to be joined.
[required]
Parameters:
--p-truncqual INTEGER Truncate sequences at the first base with the
Range(0, None) specified quality score value or lower. [optional]
--p-minlen INTEGER Sequences shorter than minlen after truncation are
Range(0, None) discarded. [default: 1]
--p-maxns INTEGER Sequences with more than maxns N characters are
Range(0, None) discarded. [optional]
--p-allowmergestagger / --p-no-allowmergestagger
Allow joining of staggered read pairs.
[default: False]
--p-minovlen INTEGER Minimum overlap length of forward and reverse reads
Range(0, None) for joining. [default: 10]
--p-maxdiffs INTEGER Maximum number of mismatches in the forward/reverse
Range(0, None) read overlap for joining. [default: 10]
--p-minmergelen INTEGER
Range(0, None) Minimum length of the joined read to be retained.
[optional]
--p-maxmergelen INTEGER
Range(0, None) Maximum length of the joined read to be retained.
[optional]
--p-maxee NUMBER Maximum number of expected errors in the joined read
Range(0.0, None) to be retained. [optional]
--p-threads INTEGER Range(0, 8, inclusive_end=True)
The number of threads to use for computation. Does
not scale much past 4 threads. [default: 1]
Outputs:
--o-joined-sequences ARTIFACT SampleData[JoinedSequencesWithQuality]
The joined sequences. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
There were some problems with the command:
(1/2) Missing option '--i-demultiplexed-seqs'.
(2/2) Missing option '--o-joined-sequences'. ("--output-dir" may also be
used)
/opt/gridview//pbs/dispatcher/mom_priv/jobs/12128946.mgt.SC:行10: --i-demultiplexed-seqs: 未找到命令
/opt/gridview//pbs/dispatcher/mom_priv/jobs/12128946.mgt.SC:行11: --o-joined-sequences: 未找到命令
求助是怎么回事