请按照课程里面的方法准备metadata文件，qiime1和qiime2 都兼容的格式,视频课程里面有讲解的：https://bdtcd.xetslk.com/s/qZRiF
还有课程里面分组名字是group和type，你的分组名字需要相应更改才行。
进行16S分析时，对样品按照分组进行分类汇总出现问题。
###我想对样品按照分组进行分类汇总，现在使用命令collapse_samples.py，对样本进行组间差异比较，具体的组别为group和type，现在出现的问题是代码无法读取我的 metadata的head line，试过很多方法无法解决。
###代码如下：
mkdir taxa_summary_group
for i in type group;do #这里的type group 来自metadata文件
collapse_samples.py -b feature_table_tax.biom -m $metadata \
--collapse_fields $i --output_mapping_fp taxa_summary_group/group.$i.txt \
--output_biom_fp taxa_summary_group/feature_table_$i.biom
#biom文件转换成表格
biom convert -i taxa_summary_group/feature_table_$i.biom \
-o taxa_summary_group/feature_table_$i.txt --to-tsv --header-key taxonomy
#分类汇总，相对丰度与绝对丰度
summarize_taxa.py -i taxa_summary_group/feature_table_$i.biom \
-o taxa_summary_group/taxa_summary_relative.$i -L 2,3,4,5,6,7
summarize_taxa.py -i taxa_summary_group/feature_table_$i.biom \
-o taxa_summary_group/taxa_summary_absolute.$i -a -L 2,3,4,5,6,7
done
##附我的metadata文件
##metadata文件使用谷歌插件keeemei检测过符合qiime2分析要求，文件格式为 .csv ，编码格式为UTF-8。
#SampleID,Group,type,Primer,Age,PH,FlySpecies,data,Des
AWGB16SAA21341083628R,MCon,MCon_1,F36/R28,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341203728R,MCon,MCon_2,F37/R28,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341323828R,MCon,MCon_3,F38/R28,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341453929R,MCon,MCon_4,F39/R29,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341572829R,MCon,MCon_5,F28/R29,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341093629R,MP,MP_1,F36/R29,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341213729R,MP,MP_2,F37/R29,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341333829R,MP,MP_3,F38/R29,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341463930R,MP,MP_4,F39/R30,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341582830R,MP,MP_5,F28/R30,NA,NA,House fly,2021/10/1,16s
AWGB16SAA21341103630R,FP,FP_1,F36/R30,60,NA,NA,2021/10/1,16s
AWGB16SAA21341223730R,FP,FP_2,F37/R30,60,NA,NA,2021/10/1,16s
AWGB16SAA21341343830R,FP,FP_3,F38/R30,60,NA,NA,2021/10/1,16s
AWGB16SAA21341473931R,FP,FP_4,F39/R31,60,NA,NA,2021/10/1,16s
AWGB16SAA21341592831R,FP,FP_5,F28/R31,60,NA,NA,2021/10/1,16s
AWGB16SAA21341113631R,EP,EP_1,F36/R31,NA,NA,NA,2021/10/1,16s
AWGB16SAA21341233731R,EP,EP_2,F37/R31,NA,NA,NA,2021/10/1,16s
AWGB16SAA21341353831R,EP,EP_3,F38/R31,NA,NA,NA,2021/10/1,16s
AWGB16SAA21341483932R,EP,EP_4,F39/R32,NA,NA,NA,2021/10/1,16s
AWGB16SAA21341602832R,EP,EP_5,F28/R32,NA,NA,NA,2021/10/1,16s
AWGB16SAA21341123632R,FWP,FWP_1,F36/R32,NA,7,NA,2021/10/1,16s
AWGB16SAA21341243732R,FWP,FWP_2,F37/R32,NA,7,NA,2021/10/1,16s
AWGB16SAA21341363832R,FWP,FWP_3,F38/R32,NA,7,NA,2021/10/1,16s
AWGB16SAA21341493933R,FWP,FWP_4,F39/R33,NA,7,NA,2021/10/1,16s
AWGB16SAA21341612833R,FWP,FWP_5,F28/R33,NA,7,NA,2021/10/1,16s
##以下是报错信息：
for i in type group;do #这里的type group 来自metadata文件
> collapse_samples.py -b feature_table_tax.biom -m /work/data/metadata.csv \
> --collapse_fields $i --output_mapping_fp taxa_summary_group/group.$i.txt\
> --output_biom_fp taxa_summary_group/feature_table_$i.biom
> #biom文件转换成表格
> biom convert -i taxa_summary_group/feature_table_$i.biom \
> -o taxa_summary_group/feature_table_$i.txt --to-tsv --header-key taxonomy
> #分类汇总，相对丰度与绝对丰度
> summarize_taxa.py -i taxa_summary_group/feature_table_$i.biom \
> -o taxa_summary_group/taxa_summary_relative.$i -L 2,3,4,5,6,7
> summarize_taxa.py -i taxa_summary_group/feature_table_$i.biom \
> -o taxa_summary_group/taxa_summary_absolute.$i -a -L 2,3,4,5,6,7
> done
Traceback (most recent call last):
File "/share/work/biosoft/python/Python2/bin/collapse_samples.py", line 93, in <module>
main()
File "/share/work/biosoft/python/Python2/bin/collapse_samples.py", line 82, in main
collapse_mode)
File "/share/work/biosoft/python/Python-v2.7.18/lib/python2.7/site-packages/qi ime/group.py", line 380, in collapse_samples
collapse_fields)
File "/share/work/biosoft/python/Python-v2.7.18/lib/python2.7/site-packages/qi ime/group.py", line 462, in _collapse_metadata
mapping_data, header, _ = parse_mapping_file(mapping_f)
File "/share/work/biosoft/python/Python-v2.7.18/lib/python2.7/site-packages/qi ime/parse.py", line 135, in parse_mapping_file
raise QiimeParseError("No header line was found in mapping file.")
qiime.parse.QiimeParseError: No header line was found in mapping file.
Usage: biom convert [OPTIONS]
Try 'biom convert -h' for help.
Error: Invalid value for '-i' / '--input-fp': File 'taxa_summary_group/feature_t able_type.biom' does not exist.
Error in summarize_taxa.py: option -i: file does not exist: 'taxa_summary_group/feature_table_type.biom'
If you need help with QIIME, see:
http://help.qiime.org
Error in summarize_taxa.py: option -i: file does not exist: 'taxa_summary_group/feature_table_type.biom'
If you need help with QIIME, see:
http://help.qiime.org
Traceback (most recent call last):
File "/share/work/biosoft/python/Python2/bin/collapse_samples.py", line 93, in <module>
main()
File "/share/work/biosoft/python/Python2/bin/collapse_samples.py", line 82, in main
collapse_mode)
File "/share/work/biosoft/python/Python-v2.7.18/lib/python2.7/site-packages/qiime/group.py", line 380, in collapse_samples
collapse_fields)
File "/share/work/biosoft/python/Python-v2.7.18/lib/python2.7/site-packages/qiime/group.py", line 462, in _collapse_metadata
mapping_data, header, _ = parse_mapping_file(mapping_f)
File "/share/work/biosoft/python/Python-v2.7.18/lib/python2.7/site-packages/qiime/parse.py", line 135, in parse_mapping_file
raise QiimeParseError("No header line was found in mapping file.")
qiime.parse.QiimeParseError: No header line was found in mapping file.
Usage: biom convert [OPTIONS]
Try 'biom convert -h' for help.
Error: Invalid value for '-i' / '--input-fp': File 'taxa_summary_group/feature_table_group.biom' does not exist.
Error in summarize_taxa.py: option -i: file does not exist: 'taxa_summary_group/feature_table_group.biom'
If you need help with QIIME, see:
http://help.qiime.org
Error in summarize_taxa.py: option -i: file does not exist: 'taxa_summary_group/feature_table_group.biom'
If you need help with QIIME, see:
http://help.qiime.org
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- gongqinglong 提出于 2024-03-21 16:25