Zymo-Research/figaro

Could not infer read orientation from filename

ekgough opened this issue · 10 comments

ekgough commented

HI I get the following output when I run this command to apply figaro to my cutadapt pimer-removed fastq giles.

python3 ~/figaro/figaro/figaro.py -o quality.limits/figaro_out -a 300 -f 19 -r 20

Traceback (most recent call last):
File "/home/ethan/figaro/figaro/figaro.py", line 218, in
main()
File "/home/ethan/figaro/figaro/figaro.py", line 208, in main
parameters = getApplicationParameters()
File "/home/ethan/figaro/figaro/figaro.py", line 17, in getApplicationParameters
return getApplicationParametersFromCommandLine()
File "/home/ethan/figaro/figaro/figaro.py", line 89, in getApplicationParametersFromCommandLine
totalFileSize = fastqAnalysis.getEstimatedFastqSizeSumFromDirectory(inputDirectory, fileNamingStandard)
File "/home/ethan/figaro/figaro/fastqAnalysis.py", line 120, in getEstimatedFastqSizeSumFromDirectory
fastqList = fastqHandler.findSamplesInFolder(path, fileNamingStandard)
File "/home/ethan/figaro/figaro/fastqHandler.py", line 538, in findSamplesInFolder
fastqFileInfoList.append(namingStandard(filePath))
File "/home/ethan/figaro/figaro/fileNamingStandards.py", line 18, in init
self.group, self.sampleNumber, self.direction = self.getSampleInfo(self.fileName)
File "/home/ethan/figaro/figaro/fileNamingStandards.py", line 61, in getSampleInfo
raise ValueError("Could not infer read orientation from filename: {}".format(fileName))
ValueError: Could not infer read orientation from filename: 1001_C_1_S39_L001_R1_001.trimmed.fastq.gz

I'm not sure why figaro is unable to infer the read orientation from 1001_C_1_S39_L001_R1_001.trimmed.fastq.gz, which is the first file in my directory.
Thank you.
Best wishes
Ethan

ekgough commented

Ok So it seems I was able to resolve this issue by renaming my fastq files to fit the Illumina naming convention for fastq files. however, now I have a different problem that I will post in a different thread.
best wishes

gailenriquez commented

how did you fix the above issue? I named my files the same way and I get the same
error "Could not infer read orientation"

ekgough commented

What do your file names look like?

gailenriquez commented
carordc commented

Hello,
I am having the same issue. My files are Illumina sequencing with the following name Bioreactor_1_S88_L001_R1_001.fastq

Thanks!

ekgough commented
carordc commented

Thank you for answering me @ekgough.

@cschu is that a solution for it?

cschu commented

@carordc Try renaming the files, removing the _001 after the _R1 or _R2 part. You could also try a different file naming standard with -F <filenamingstandard>, but I'm not sure whether your format is covered. I think the _ in Bioreactor_1 may cause a problem for the illumina naming standard.

carordc commented

@carordc Try renaming the files, removing the _001 after the _R1 or _R2 part. You could also try a different file naming standard with -F <filenamingstandard>, but I'm not sure whether your format is covered. I think the _ in Bioreactor_1 may cause a problem for the illumina naming standard.

Thanks! I took out the _001 and the beggining, and it worked. :)

cschu commented

Glad it worked!