[Bug]: issue running binningVis when maxbin doesn't generate output

[Panda-smile]

Hello，professor！ I got an error when running the following program. How can I solve it?

code：yes | bash metaGEM.sh -t binningVis --local

erro: Warning message:
Package 'ggplot2' was built with R version 4.4.3
Error in $<-.data.frame(*tmp*, binner, value = "MaxBin2"):
Replacement data has 1 row, but data has 0
Calls: $<- -> $<-.data.frame

Generating refined_bins.stats file containing bin ID, number of contigs, and length ...
Reading bin sample1/metawrap_50_10_bins/bin.1.fa ... Contigs: 958 , Length: 2069761
Reading bin sample1/metawrap_50_10_bins/bin.2.fa ... Contigs: 70 , Length: 2009255
Reading bin sample1/metawrap_50_10_bins/bin.3.fa ... Contigs: 374 , Length: 1999270
Reading bin sample1/metawrap_50_10_bins/bin.4.fa ... Contigs: 399 , Length: 2050835
Reading bin sample1/metawrap_50_10_bins/bin.5.fa ... Contigs: 80 , Length: 2027400
Reading bin sample1/metawrap_50_10_bins/bin.6.fa ... Contigs: 184 , Length: 2506080
Reading bin sample1/metawrap_50_10_bins/bin.7.fa ... Contigs: 170 , Length: 2421934
Generating CheckM summary files across samples: concoct.checkm, metabat.checkm, maxbin.checkm, and refined.checkm ...
Generating reassembled_bins.stats file containing bin ID, number of contigs, and length ...
Reading bin sample1/reassembled_bins/bin.1.permissive.fa ... Contigs: 902 , Length: 2071398
Reading bin sample1/reassembled_bins/bin.2.orig.fa ... Contigs: 70 , Length: 2009255
Reading bin sample1/reassembled_bins/bin.3.strict.fa ... Contigs: 237 , Length: 1934357
Reading bin sample1/reassembled_bins/bin.4.orig.fa ... Contigs: 399 , Length: 2050835
Reading bin sample1/reassembled_bins/bin.5.orig.fa ... Contigs: 80 , Length: 2027400
Reading bin sample1/reassembled_bins/bin.6.orig.fa ... Contigs: 184 , Length: 2506080
Reading bin sample1/reassembled_bins/bin.7.permissive.fa ... Contigs: 135 , Length: 2428472
Done reading metawrap reassembled bins ...
Generating CheckM summary file reassembled.checkm across samples for reassembled bins ...
Done generating all statistics files for binning results ... running plotting script ...

载入程序包：‘dplyr’

The following object is masked from ‘package:gridExtra’:

combine

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

警告信息:
程序包‘ggplot2’是用R版本4.4.3 来建造的
错误于$<-.data.frame(*tmp*, binner, value = "MaxBin2"):
替换数据里有1行，但数据有0
Calls: $<- -> $<-.data.frame
停止执行
[Sun Aug 17 16:20:42 2025]
Error in rule binningVis:
jobid: 0
output: /public/home/zhanglj/metagem/metaGEM/workflow/stats/reassembled_bins.stats, /public/home/zhanglj/metagem/metaGEM/workflow/stats/binningVis.pdf

[franciscozorrilla]

Hi Zhang, the error message seems to suggest that MaxBin2 did not generate any MAGs for some sample(s). Could you double check if this is the case? If so then I would recommend to modify the binningVis.R script by removing the data preparation sections related to MaxBin2.

[Panda-smile]

It is indeed the case, professor, as you said. I would like to ask how to correct the complete and contamination parameters?

…

------------------ 原始邮件 ------------------ 发件人: "franciscozorrilla/metaGEM" ***@***.***>; 发送时间: 2025年8月20日(星期三) 下午3:53 ***@***.***>; ***@***.******@***.***>; 主题: Re: [franciscozorrilla/metaGEM] [Bug]: _______________ (Issue #178) franciscozorrilla left a comment (franciscozorrilla/metaGEM#178) Hi Zhang, the error message seems to suggest that MaxBin2 did not generate any MAGs for some sample(s). Could you double check if this is the case? If so then I would recommend to modify the binningVis.R script by removing the data preparation sections related to MaxBin2. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[franciscozorrilla]

Please note that these visualization scripts are very basic and I wrote them a long time ago (e.g. as you can see they cannot handle cases where no MAGs are generated). Feel free to use them for a quick visualization, but I would recommend that you modify them as needed to suit your needs.

If you want to generate the visualization of binning for your results (i.e. excluding maxbin2 since it did not generate any MAGs), then you will have to make the following modifications to the binningVis.R script:

• Delete or comment out the following lines:

metaGEM/workflow/scripts/binningVis.R

Lines 21 to 28 in 8609ad6

	maxbinCheckm = read.delim("maxbin.checkm",stringsAsFactors = FALSE,header = FALSE)
	colnames(maxbinCheckm) = c("bin","completeness","contamination","GC","lineage","N50","size","set")
	maxbinBins= read.delim("maxbin_bins.stats",stringsAsFactors = FALSE,header = FALSE, sep = " ")
	colnames(maxbinBins) = c("bin","contigs","length")
	maxbin = left_join(maxbinCheckm,maxbinBins%>%select(-length),by="bin") %>% filter(contamination<=10,completeness>=50)%>% distinct() %>% select(-set)
	maxbin$contigs = as.numeric(maxbin$contigs)
	maxbin$sample = gsub("\\..*$","",maxbin$bin)
	maxbin$binner = "MaxBin2"

metaGEM/workflow/scripts/binningVis.R

Line 65 in 8609ad6

geom_density(data=maxbin,aes(completeness,color="maxbin2")) +

metaGEM/workflow/scripts/binningVis.R

Line 75 in 8609ad6

geom_density(data=maxbin,aes(contamination,color="maxbin2")) +

metaGEM/workflow/scripts/binningVis.R

Line 85 in 8609ad6

geom_density(data=maxbin,aes(size,color="maxbin2")) +

metaGEM/workflow/scripts/binningVis.R

Line 95 in 8609ad6

geom_density(data=maxbin,aes(contigs,color="maxbin2")) +

• Modify this line by removing the maxbin dataframe from the rbind command:

metaGEM/workflow/scripts/binningVis.R

Line 51 in 8609ad6

rbind(concoct,metabat,maxbin,refined,reassembled) %>% group_by(binner,sample) %>% summarize(count=n()) -> bins

[Panda-smile]

Thank you very much for your careful guidance. 

…

------------------ 原始邮件 ------------------ 发件人: "franciscozorrilla/metaGEM" ***@***.***>; 发送时间: 2025年8月20日(星期三) 下午5:47 ***@***.***>; ***@***.******@***.***>; 主题: Re: [franciscozorrilla/metaGEM] [Bug]: _______________ (Issue #178) franciscozorrilla left a comment (franciscozorrilla/metaGEM#178) Please note that these visualization scripts are very basic and I wrote them a long time ago (e.g. as you can see they cannot handle cases where no MAGs are generated). Feel free to use them for a quick visualization, but I would recommend that you modify them as needed to suit your needs. If you want to generate the visualization of binning for your results (i.e. excluding maxbin2 since it did not generate any MAGs), then you will have to make the following modifications to the binningVis.R script: Delete or comment out the following lines: https://github.com/franciscozorrilla/metaGEM/blob/8609ad6bcf040807df0928705d91b0ae31923259/workflow/scripts/binningVis.R#L21-L28 https://github.com/franciscozorrilla/metaGEM/blob/8609ad6bcf040807df0928705d91b0ae31923259/workflow/scripts/binningVis.R#L65 https://github.com/franciscozorrilla/metaGEM/blob/8609ad6bcf040807df0928705d91b0ae31923259/workflow/scripts/binningVis.R#L75 https://github.com/franciscozorrilla/metaGEM/blob/8609ad6bcf040807df0928705d91b0ae31923259/workflow/scripts/binningVis.R#L85 https://github.com/franciscozorrilla/metaGEM/blob/8609ad6bcf040807df0928705d91b0ae31923259/workflow/scripts/binningVis.R#L95 Modify this line by removing the maxbin dataframe from the rbind command: https://github.com/franciscozorrilla/metaGEM/blob/8609ad6bcf040807df0928705d91b0ae31923259/workflow/scripts/binningVis.R#L51 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>