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

Infrastructure and utilities KneadData
1

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

2

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

3

Hi @sagun,

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

Regards,
Amit

4

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

5

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

Regards,
Sagun

6

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.

7

@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

8

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.

9

Hi bro,
I got same error like you,but when i tap --bypass-trim and --bypass trf,everything work out( My data has been processed by fastp).

10

I answered this elsewhere on the forum, but tldr: The sequence names apparently must have .R1. or .R2. as the input file name.

11

Hello, It sounds like if you are seeing the new options that you have the latest version installed. Is it possible you are running out of disk space?

Thank you,
Lauren

12

Hi, I ahve the same problem, PE reads trimmed using bbduk. Using --bypass-trim failed (same error can’t write). trf is still actif, will try without trf.
Whit version 0.11.0 bypass-trim and trf actif are working?
Thanks

13

Yes, they should be. Please post if you run into any issues.

Thanks!
Lauren