Comments (23)
I'm using the Docker image btw.
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Hi, thanks for reporting. Are you using the 0.3 release or did you clone the repository?
from metaphage.
I cloned into the repository
from metaphage.
For
The records, I just tested the whole pipeline (both v0.3 and last commit) using docker and worked. Hence the issue is probably related to your specific dataset/metadata file. I will check a way to gather more info
from metaphage.
Did you create a "configuration file" using the provided "newProject.py" script?
See https://mattiapandolfovr.github.io/MetaPhage/new
Can you please upload the configuration file used?
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from metaphage.
Hi Lonnie, could you please provide your metadata and config file? I fail to find them in the mail attachments.
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from metaphage.
Hi again,
for some reason the mail has no attachments. Upload the files on Google drive and send me the folder link, thank you.
Regards
Mattia
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See https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/attaching-files to upload directly on github issue (not via mail).
Cheers
a
from metaphage.
Here are the config and metadata files:
from metaphage.
Hi Lonnie,
your Sample names in the metadata.csv are numbers, which cause the sample_data() function to add the "sa" string in front. This function is used to create the phyloseq object, therefore the error: phyloseq tries to match the sample names in your count table (1 2 3 4) to these modified names (sa1, sa2, sa3, sa4), failing. I would suggest you to rename the samples adding some characters (e.g. sample1, sample2 etc).
Regards
Mattia
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from metaphage.
Hi Mattia,
Unfortunately the change to the metadata file did not resolve the issue. Phyloseq still won't run. Please see the error below:
[a5/df1fca] process > summary (megahit) [100%] 1 of 1 ✔
[c1/fac0fa] process > file_chopper (megahit) [100%] 1 of 1 ✔
[- ] process > taxonomy_table (megahit) -
[30/f61abd] process > heatmap (megahit) [100%] 1 of 1, failed: 1 ✘
[- ] process > alpha_diversity [ 0%] 0 of 1
[- ] process > betadiversity [ 0%] 0 of 1
[- ] process > violin_plots [ 0%] 0 of 1
[- ] process > multiqc -
Error executing process > 'heatmap (megahit)'
Caused by:
Process heatmap (megahit)
terminated with an error exit status (1)
Command executed:
Rscript /home/imbm-bioinformatics/Downloads/MetaPhage-0.3.0/bin/Rscript/heatmap.R count_table.csv taxonomy_table.csv metadata.csv library
Command exit status:
1
Command output:
(empty)
Command error:
Error in validObject(.Object) : invalid class “otu_table” object:
OTU abundance data must have non-zero dimensions.
Calls: filter_taxa ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Work dir:
/home/imbm-bioinformatics/Downloads/MetaPhage-0.3.0/work/30/f61abd786bdda3c28b76651a0f8d80
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
Here are the new metadata and config files as well as the taxonomy and count tables:
[nextflow.txt](https://github.com/MattiaPandolfoVR/MetaPhage/files/
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from metaphage.
Hi Lonnie, sorry for the late reply,
No need to install different distros, the problem was related to the relative abundance filter applied to the phyloseq object, which i fixed. I already updated the code, download again the bin/Rscript folder only and launch MetaPhage (use -resume when you launch it to start from where it stopped). I hope this fix the issue!
Regards
Mattia
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from metaphage.
Hi Mattia,
alpha diversity runs fine, however the heatmap and beta diversity still have issues.
The beta diversityy error is as follows:
Error executing process > 'betadiversity (megahit)'
Caused by:
Process betadiversity (megahit)
terminated with an error exit status (1)
Command executed:
Rscript /home/imbm-bioinformatics/Downloads/MetaPhage-0.3.0/bin/Rscript/beta_diversity.R count_table.csv taxonomy_table.csv metadata.csv Site
Command exit status:
1
Command output:
(empty)
Command error:
Error in eval(expr, data, expr_env) : object 'Axis.2' not found
Calls: ... -> -> eval_expr -> eval -> eval
Execution halted
Whereas the heatmap error is:
Error executing process > 'heatmap (megahit)'
Caused by:
Process heatmap (megahit)
terminated with an error exit status (1)
Command executed:
Rscript /home/imbm-bioinformatics/Downloads/MetaPhage-0.3.0/bin/Rscript/heatmap.R count_table.csv taxonomy_table.csv metadata.csv Site
Command exit status:
1
Command output:
(empty)
Command error:
Error in cluster::pam(sdata, k, diss = diss, ...) :
Number of clusters 'k' must be in {1,2, .., n-1}; hence n >= 2
Calls: %>% ... heatmaply.default -> heatmapr -> find_k -> pamk ->
Execution halted
The violin_plots error is:
Error executing process > 'violin_plots (megahit)'
Caused by:
Process violin_plots (megahit)
terminated with an error exit status (1)
Command executed:
Rscript /home/imbm-bioinformatics/Downloads/MetaPhage-0.3.0/bin/Rscript/violin_plot.R count_table.csv taxonomy_table.csv metadata.csv Site
Command exit status:
1
Command output:
(empty)
Command error:
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: shhh -> withCallingHandlers -> source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'bin/Rscript/filter&CSSnormalize.R': No such file or directory
Execution halted
Regards
Lonnie
from metaphage.
Hi Lonnie,
Your problem may be related to that "cannot open file 'bin/Rscript/filter&CSSnormalize.R': No such file or directory".
Are you sure you downloaded again the /bin/Rscript folder?
Regards,
Mattia
from metaphage.
Hi Mattia,
Yes, that is the issue for violin plots, and it's easy enough to fix by editing the R.script file, but the other two are my main concern.
Regards
Lonnie
from metaphage.
Hi there,
The problem was related to the sourcing of the filtering function. I updated the Rscripts using it, and tested (again) everything. It seems to work flawless, so download again the whole bin/Rscript folder to have the updated version. Let me know if the issue persist.
Regards,
Mattia
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Related Issues (20)
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- Issue with vcontact2 classification HOT 5
- Error - Inphared database - vcontact2 Jun2022 HOT 1
- Unable to build the MetaPhage Environment HOT 3
- virsorter error HOT 1
- Out of memory error at the Qualimap bamqc step HOT 2
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- Does skipping graphanalyzer step lead to errors in the next steps? HOT 1
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