Could not infer read orientation from filename

[ekgough]

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]

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]

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]

What do your file names look like?

[gailenriquez]

Hi sorry for the late response. My filename looks like this: MB002B_S157_L001_R1_001.fastq.gz and MB002B_S157_L001_R2_001.fastq.gz

…

________________________________ From: ekgough ***@***.***> Sent: Tuesday, October 18, 2022 7:31 AM To: Zymo-Research/figaro ***@***.***> Cc: Enriquez, Gail Hillary ***@***.***>; Comment ***@***.***> Subject: Re: [Zymo-Research/figaro] Could not infer read orientation from filename (Issue #48) What do your file names look like? — Reply to this email directly, view it on GitHub<#48 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXI24MPF2THXGGZDNGYDK5DWD2KAXANCNFSM5VZK4G2Q>. You are receiving this because you commented.Message ID: ***@***.***>

[carordc]

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]

I'm sorry I did not get a response to my query and I was not able to resolve the issue I was having.

…

On Tue, Aug 13, 2024 at 10:31 AM carordc ***@***.***> wrote: Hello, I am having the same issue. My files are Illumina sequencing with the following name Bioreactor_1_S88_L001_R1_001.fastq Thanks! — Reply to this email directly, view it on GitHub <#48 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZESYYU27TJEQDGHMVRBMT3ZRIKD3AVCNFSM6AAAAABMONDROGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOBWGQYDMNRRGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[carordc]

Thank you for answering me @ekgough.

@cschu is that a solution for it?

[cschu]

@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]

@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]

Glad it worked!