把输入文件截图看看的，你这个metadata文件列分割符不是tab键，对比下课程里面的示例文件；
16S 差异比较使用compare_errorbar.r的时候报错
我用这个代码是他的前一步不报错，但是这一步报错，代表我的分组信息这些都是准确的
这个代码不报错
for i in {2..6};do
Rscript $scriptdir/meta_stat.r -i ../05.export_data/taxa_summary/absolute_abundance/feature_table_tax_L$i.txt \
-m $metadata -t Group \
-a WSD_Lig_PPI -b WSD_PPI \
-o meta_stat --name WSD_Ligatur_vsKD_Ligatur_Lppi$i
done
#但是这个代码就开始报错了
for m in "ALDEx2" "DESeq2" "edgeR" "limma.voom" "metagenomeSeq" "LinDA" "Maaslin2" "Lefser" ;do
table=../05.export_data/taxa_summary/absolute_abundance/feature_table_tax_L6.txt
#table=../05.export_data/feature_table.txt
Rscript $scriptdir/compare_errorbar.r -i $table \
-m $metadata -t Group \
-a WSD_Lig_PPI -b WSD_PPI \
--daa_method $m \
--p_values_threshold 1 \
--top 20 \
-o compare_errorbar --prefix WSD_Ligatur_vsKD_Ligatur_ppiL6
done
# 报错信息如下
for m in "ALDEx2" "DESeq2" "edgeR" "limma.voom" "metagenomeSeq" "LinDA" "Maaslin2" "Lefser" ;do
> table=../05.export_data/taxa_summary/absolute_abundance/feature_table_tax_L6.txt
> #table=../05.export_data/feature_table.txt
> Rscript $scriptdir/compare_errorbar.r -i $table \
> -m $metadata -t Group \
> -a WSD_Lig_PPI -b WSD_PPI \
> --daa_method $m \
> --p_values_threshold 1 \
> --top 20 \
> -o compare_errorbar --prefix WSD_Ligatur_vsKD_Ligatur_ppiL6
> done
--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/
--> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index
Failed to create bus connection: No such file or directory
── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.3 ✔ purrr 1.0.2
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.4 ✔ tidyr 1.3.0
✔ lubridate 1.9.3
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Rows: 18 Columns: 7
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): KOT, date, Group
dbl (4): #SampleID, MouseNR, Plate, DES
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in `select()`:
! Can't subset columns with `metaData[, 1, drop = T]`.
✖ Can't convert from `metaData[, 1, drop = T]` <double> to <integer> due to loss of precision.
Backtrace:
▆
1. ├─dplyr::select(abundance_data, metaData[, 1, drop = T])
2. ├─dplyr:::select.data.frame(abundance_data, metaData[, 1, drop = T])
3. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
4. │ └─tidyselect:::eval_select_impl(...)
5. │ ├─tidyselect:::with_subscript_errors(...)
6. │ │ └─rlang::try_fetch(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ └─tidyselect:::vars_select_eval(...)
9. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
10. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
11. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
12. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
13. │ └─tidyselect:::as_indices_sel_impl(...)
14. │ └─tidyselect:::as_indices_impl(...)
15. │ └─vctrs::vec_as_subscript(x, logical = "error", call = call, arg = arg)
16. └─rlang::cnd_signal(x)
Execution halted
--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/
--> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index
Failed to create bus connection: No such file or directory
── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.3 ✔ purrr 1.0.2
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.4 ✔ tidyr 1.3.0
✔ lubridate 1.9.3
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Rows: 18 Columns: 7
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): KOT, date, Group
dbl (4): #SampleID, MouseNR, Plate, DES
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in `select()`:
! Can't subset columns with `metaData[, 1, drop = T]`.
✖ Can't convert from `metaData[, 1, drop = T]` <double> to <integer> due to loss of precision.
Backtrace:
▆
1. ├─dplyr::select(abundance_data, metaData[, 1, drop = T])
2. ├─dplyr:::select.data.frame(abundance_data, metaData[, 1, drop = T])
3. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
4. │ └─tidyselect:::eval_select_impl(...)
5. │ ├─tidyselect:::with_subscript_errors(...)
6. │ │ └─rlang::try_fetch(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ └─tidyselect:::vars_select_eval(...)
9. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
10. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
11. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
12. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
13. │ └─tidyselect:::as_indices_sel_impl(...)
14. │ └─tidyselect:::as_indices_impl(...)
15. │ └─vctrs::vec_as_subscript(x, logical = "error", call = call, arg = arg)
16. └─rlang::cnd_signal(x)
Execution halted
--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/
--> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index
Failed to create bus connection: No such file or directory
── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.3 ✔ purrr 1.0.2
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.4 ✔ tidyr 1.3.0
✔ lubridate 1.9.3
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Rows: 18 Columns: 7
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): KOT, date, Group
dbl (4): #SampleID, MouseNR, Plate, DES
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in `select()`:
! Can't subset columns with `metaData[, 1, drop = T]`.
✖ Can't convert from `metaData[, 1, drop = T]` <double> to <integer> due to loss of precision.
Backtrace:
▆
1. ├─dplyr::select(abundance_data, metaData[, 1, drop = T])
2. ├─dplyr:::select.data.frame(abundance_data, metaData[, 1, drop = T])
3. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
4. │ └─tidyselect:::eval_select_impl(...)
5. │ ├─tidyselect:::with_subscript_errors(...)
6. │ │ └─rlang::try_fetch(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ └─tidyselect:::vars_select_eval(...)
9. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
10. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
11. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
12. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
13. │ └─tidyselect:::as_indices_sel_impl(...)
14. │ └─tidyselect:::as_indices_impl(...)
15. │ └─vctrs::vec_as_subscript(x, logical = "error", call = call, arg = arg)
16. └─rlang::cnd_signal(x)
Execution halted
--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/
--> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index
Failed to create bus connection: No such file or directory
── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.3 ✔ purrr 1.0.2
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.4 ✔ tidyr 1.3.0
✔ lubridate 1.9.3
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
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- Vegetable 提出于 2024-07-23 03:16