Galaxy StringTie error
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5 weeks ago
trkfs • 0

Hello

I've been running tools on Galaxy (https://usegalaxy.org) today to analyze bulk RNA-seq data following this pipeline (https://youtu.be/KVh98S89yUU?si=jvBNvbZ-stVoz9-k). I've run StringTie on two different datasets and I keep getting this error while trying to generate the Gene and Transcript counts files.

Dataset Error Report

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.2+galaxy0.
Details

Tool generated the following standard error:

/usr/local/bin/prepDE.py:72: SyntaxWarning: invalid escape sequence '\-'
  RE_COVERAGE=re.compile('cov "([\-\+\d\.]+)"')
/usr/local/bin/prepDE.py:75: SyntaxWarning: invalid escape sequence '\-'
  RE_GFILE=re.compile('\-G\s*(\S+)') #assume filepath without spaces..

I have sent a bug report to the Galaxy administrator but while I wait for their reply, I was wondering if anybody else has faced the same problem or if somebody has some answers. Is this an issue with my dataset or with the StringTie tool?

stringtie galaxy • 351 views
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I have sent a bug report to the Galaxy administrator

If you have not done so please post this in Galaxy help forum for directed help: https://help.galaxyproject.org/

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will do, thank you

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I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add an invalid escape character in a Python string literal. For example of one that works:

>>>print("sample \t code")
sample        code

So, it is picky about that letters/characters you can add after a \

When you are inputting your files into galaxy, or choosing an option, do you see anywhere that has a \-? I am wondering if maybe this is something conserved within Galaxy and gives this error when you add "\-" into a string. When I do print("\-") in Python at least, it prints out as:

>>>print("\-")
\-

so this would probably be unique to Galaxy.

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Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank you for your input anyway!

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