Code problems

[iquasere]

Code problems

[transcript]

Hello,

The purpose of the bash expression echo ${out_path##*/} is to cut out all preceding path elements.

If the file_path here is 1_starting_files/control_1_TINY.merged, for example, this bash expression will return control_1_TINY.merged.

I'm not sure why you're having issues identifying the functional and taxonomic information of the genes. Is this a failure in the master script? Is this occurring on Step 5, when generating the functional results from the RefSeq database? Are you using the default database (RefSeq_bac)?

Hopefully I can help you fix these issues.

[transcript]

I am making some updates to the tool, but this shouldn't be causing issues such as these you're reporting.

[utpalh]

I run the program, and got the following problem,

Calculating DESeq results for hierarchy level 1
Error in row.names<-.data.frame(*tmp*, value = value) :
duplicate 'row.names' are not allowed
Calls: rownames<- ... rownames<- -> row.names<- -> row.names<-.data.frame
In addition: Warning message:
non-unique values when setting 'row.names': ‘’, ‘1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.11.54)’, ‘1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase (EC 1.3.1.25)’, ‘1,2-dihydroxynaphthalene dioxygenase’, ‘12-oxophytodienoate reductase (OPR3)(DDE1)’, ‘1,4-alpha-glucan branching enzyme (EC 2.4.1.18)’, ‘1,4-alpha-glucan (glycogen) branching enzyme, GH-13-type (EC 2.4.1.18)’, ‘1,4-dihydroxy-2-naphthoate octaprenyltransferase (EC 2.5.1.74)’, ‘16 kDa heat shock protein A’, ‘16 kDa heat shock protein B’, ‘16S rRNA m(5)C 967 methyltransferase (EC 2.1.1.-)’, ‘16S rRNA processing protein RimM’, ‘1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51)’, ‘1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267)’, ‘1-deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7)’, ‘1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (EC 1.17.7.1)’, ‘1-phosphofructokinase (EC 2.7.1.56)’, ‘1-pyr [... truncated]
Execution halted
can you let me know how to sort the problem

[transcript]

Hi utpalh,

Did this error happen while running the master_script.sh? Or were you running one of the R scripts separately?

Just from the error that you've pasted in, it looks like you're trying to run the Subsystems_DESeq_stats.R script, but it's having issues with the raw counts table. Could you upload the raw counts table that you received to this issue? This should be located in your Step 2 folder.

[utpalh]

raw counts
control_1_Healthy 21092913
control_2_Healthy 20298464
control_3_Healthy 20078549
experimental_4_HLB 19632654
experimental_5_HLB 20712965
experimental_6_HLB 22204048

I run DESeq for REfseq, no problem but for the subsystems_results i have the error

I have run the master_script.sh, the error came while running the following lines in it.
Rscript $R_programs/Subsystems_DESeq_stats.R -I $starting_location/step_5_output/Subsystems_results/receipts/ -O Subsystems_level-1_DESeq_results.tab -L 1 -R $starting_location/step_2_output/raw_counts.txt

I tried both the file location with subsystem result files.

1. step_5_output/Subsystems_results/
2. step_5_output/Subsystems_results/receipts/

Output

[1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename -L level (1,2,3,4)"
Working directory is /home/utpal/Documents/samsa2/step_5_output/Subsystems_results/receipts/
Saving results as Subsystems_level-1_DESeq_results.tab
Calculating DESeq results for hierarchy level 1
Error in row.names<-.data.frame(*tmp*, value = value) :
duplicate 'row.names' are not allowed
Calls: rownames<- ... rownames<- -> row.names<- -> row.names<-.data.frame
In addition: Warning message:

[transcript]

Hmm, the counts file contents you posted look fine. So that's not the issue.

You shouldn't be using the receipts location; this should be calling the files in $STEP_5/Subsystems_results. Is there a chance you could attach a couple of the results files to this issue?

(You can attach files to a Github comment by dragging them into the text box or using the link at the bottom to select them.)

If you cannot do this, I can try making some more explicit merge commands in the R script and uploading that for you to try in place of yours, but I'm not sure why it's encountering this issue. I am not seeing this in my tests.

[utpalh]

I uploaded 4 files, Check if there is anything you find that are not correct
4 files.zip

[transcript]

Ah, that's resolved it!

It looks like the R script was properly converting blank hierarchy entries into "NO HIERARCHY", but was missing when an entry is instead classified as "N/A". One line fix, and the script now runs without any problems.

I've pushed an update, but I'm also attaching the R script here. If you replace your "Subsystems_DESeq_stats.R" file with this one, things should work. (You'll have to gunzip the file, because Github won't let me share a script file directly, but will if it's gzipped. Go figure.)

Subsystems_DESeq_stats.R.gz

[utpalh]

Thanks Sam its working fine now

[utpalh]

I came upon the following error while processing for Level 2 subsystem and level 4 subsystem

[1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename -L level (1,2,3,4)"
Working directory is /home/utpal/Documents/samsa2/step_5_output/Subsystems_results/
Saving results as Subsystems_level-2_DESeq_results.tab
Calculating DESeq results for hierarchy level 2
Error in setnames(x, value) :
Can't assign 4 names to a 3 column data.table
Calls: colnames<- ... colnames<- -> names<- -> names<-.data.table -> setnames
Execution halted
[1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename -L level (1,2,3,4)"
Working directory is /home/utpal/Documents/samsa2/step_5_output/Subsystems_results/
Saving results as Subsystems_level-1_DESeq_results.tab
Calculating DESeq results for hierarchy level 4
Error in row.names<-.data.frame(*tmp*, value = value) :
duplicate 'row.names' are not allowed
Calls: rownames<- ... rownames<- -> row.names<- -> row.names<-.data.frame
In addition: Warning message:
non-unique value when setting 'row.names': ‘NO HIERARCHY’
Execution halted