Paired end data showing error on --bypass-trim option

Hi,

I am using KneadData v0.10.0, when I am giving option “–bypass-trim” for single data it is running fine but when I am using for paired end data it is showing error

Initial number of reads ( /output/reformatted_identifiersq0owrl0l_fastq_r1 ): 25000.0
Initial number of reads ( /output/reformatted_identifierstorf93m__fastq_r2 ): 25000.0
Bypass trimming
Total reads after trimming ( /output/reformatted_identifiersq0owrl0l_fastq_r1 ): 25000.0
Total reads after trimming ( /output/reformatted_identifierstorf93m__fastq_r2 ): 25000.0
ERROR: Unable to write file: /output/reformatted_identifiersq0owrl0l_fastq_r1

I have also tried with different data sets but I am getting same error. Kindly let me know how to resolve this error.
Thank you!
Regards,
Amit

Hi @amit ,

Thank you for reaching out to bioBakery Lab. Can you try updating kneaddata to v0.11.0.
Please note that the input options has changed: kneaddata · biobakery/biobakery Wiki · GitHub

If you still face the same error, please let us know and we will get it fixed.

Regards,
Sagun

Hi @sagun,

Thank you so much for the quick reply. I will update and let you know.

Regards,
Amit

Hi @sagun,

I followed the link and the steps. After installing it is still showing v0.10.0 but the input option has changed. Now it is showing as -i1, -i2 and -un. I am getting same error.

Regards,
Amit

Hi @amit ,
Thanks for the update. I will take a look at this and update you.

Regards,
Sagun

Hi @sagun,

v 0.11 seems to be self-reporting as 0.10, had the same issue. If you check with pip, it will show version 0.11 being installed. Instead i1 and i2 try input1 and input2.

@R_S Not sure if @sagun tried, but it didn’t work with 0.11 using i1 or input1 when I try to bypass trimming

Hi I think I’m having similar issues, at least to some degree.
I think I previously had v0.10.0 when I noticed that PE runs were not proceeding but no errors were thrown, it just kind of hung, plus the input controls were definitely not clear (since I know the update has changed this, but the documentation is very inconsistent, sometimes saying -i1 -i2, or just --input).

I just attempted a reinstall, first using pip, which said nothing to do, kneaddata already found, but my version was still saying v0.10.0. Then I just did with git clone, succeeded, and version still reports v0.10.0.
Is this incorrect?

Only one line in the screen output from the install indicates v0.11.0:
Copying kneaddata.egg-info to /usr/local/lib/python3.6/site-packages/kneaddata-0.11.0-py3.6.egg-info

I’m trying again with PE data using --input1 and --input2, and so far it is stuck on "Reformatting file sequence identifiers … " with almost no activity on my processor.