read2 -O "is a folder, not a file, quit now"

[symbiologist]

Hi all,

Trying to run fastp on a PE150 sample.

Here is the exact line I'm running:
fastp -i Emx1_1_11_CTRL_USPD16084012-4_HHG33BBXX_L6_1.fq.gz -I Emx1_1_11_CTRL_USPD16084012-4_HHG33BBXX_L6_2.fq.gz -o r1.fq.gz -O r2.fq.gz

Here is the error I get:
ERROR: 'r2.fq.gz' is a folder, not a file, quit now

I have no problems running fastp on either of these fastq files in single-end mode. Also tried using --out2 instead of -O, I get the same result.

Any idea how I can get this to run?

Best,
David

[sailingnn]

I've got the same problem here. The fastp version is 0.12.6.

[sfchen]

I am doing the tests, wait for 10 minutes.

[sfchen]

Reproduced, seems like a bug on some Linux systems. I will fix it in 10 minutes.

[sfchen]

That's caused by a bug of C system API, which acts differently on different Linux systems.

I just fixed it, could you please try the latest v0.13.1 ?

BTW, what are your systems?

[symbiologist]

Thanks! Seems to be working now. I am running Ubuntu 16.04.4 LTS.