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error while running run_DESeq_stats.R #81
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Hi @rachel1898, I got the same error message when I was running SAMSA2 and I was able to fix it so I might be able to help. Did you make sure your filenames all start with |
Question for the developers: Was SAMSA2 written expecting the sample names to be strictly numeric? I ran into two errors in raw_counts_table$X2 <- as.numeric(as.character(raw_counts_table$X2)) So then when those values got used as column names, it made Later in the script I had another issue with my count values being turned into factors and introducing more NAs, which I think also might have happened because of my sample names not being numeric. I was able to fix the problem by modifying a few lines of the script, but I was wondering if maybe the real issue was that I misunderstood the usage instructions and should have changed my filenames before running the pipeline to avoid any problems. Can you provide some guidance on what characters are allowed to be in the input filenames? |
Hello, No, SAMSA2 wasn't written to explicitly expect numeric samples (although I believe that whitespace characters can sometimes mess things up). I suspect what's happening is that, if the samples are too different, the One useful check: look at the Another option is to run this in RStudio and see if any of the intermediate tables look invalid. Finally, if none of this is able to yield results or if you want me to look at one or two of the input files to see if I spot any inconsistencies, you could drop me an email (swestreich@gmail.com) with one or two attached. Sorry to hear you're having issues with my pipeline, and I hope I can resolve them! |
Hi @transcript, thank you for the thoughtful response! I have a reproducible example of the behavior that @rachel1898 and I observed: git clone https://github.com/transcript/samsa2.git
cd samsa2
# Use the sample files, but remove an underscore
# control_1_TINY_R1.fastq --> control_1TINY_R1.fastq
cp -r sample_files_paired-end/1_starting_files input_files
for f in input_files/*; do mv $f ${f/_TINY/TINY}; done
bash setup_and_test/package_installation.bash
bash setup_and_test/full_database_download.bash
bash bash_scripts/master_script.sh
# run_DESeq_stats.R fails Error message:
The problem is that in order to parse the information out of the filenames,
However, if the filenames do not follow that pattern and the second field is not numeric, NA's are induced:
I have a fix that allows more flexibility in the filenames. Are you open to pull requests? |
Fix for issue transcript#81. In a nutshell, sample names are now extracted more precisely from filenames so that file naming can be more flexible.
Fix by @lisakmalins added! |
Hello,
I had an error when I try to run DESeq_stats through master_script.sh
Steps 1 to 5 went perfectly but when it gets to step 6 I had the following error:
[1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename"
Working directory is /home/samsa2/output/step_5_output/RefSeq_results/org_results
Error in match.names(clabs, names(xi)) :
names do not match previous names
Calls: rbind ... eval -> eval -> eval -> rbind -> rbind -> match.names
In addition: Warning message:
NAs introduced by coercion
Execution halted
'Rscript /home/samsa2/R_scripts/run_DESeq_stats.R -I /home/samsa2/output/step_5_output/RefSeq_results/org_results -O RefSeq_org_DESeq_results.tab -R /home//samsa2/output/step_2_output/raw_counts.txt' exited with non-zero status 1
I think the problem is that control files doesn't have the same column names but as I run the master_script.sh I could not figure out what went wrong. Would you guide me through this?
Thanks!!
Raquel
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