使用qiime vsearch join-pairs报错--i-demultiplexed-seqs: 未找到命令

2024-03-16 10:46:08 649 阅读 AI 写同款 · GEO 优化AI 选题数据监测一键分发 ›

基于qiime2的16S数据分析全流程：从导入数据到下游分析一条龙基于qiime2的16s测序数据分析分析激活qiime环境我已经把上面这句代码放在了.bashrc里面，因此激活qiime2环境只需要运行activate_qiime即可/bin/bash# 设置目录路径# 输出表头 echo -e "sample-id\tforward-absolute-filepath\treverse-absolute-filepath"# 遍历_R1和_R2文件do # 检查R1文件是否存在then# 获取样本ID（去掉_R1.fastq.gz）阅读详情

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

...全文