FastUniq error - Error in open left fastq file site1_R1_P_qtrim.fq for read!

Question

[brenna.stanford1]

Hi everyone,

I am attempting to use FastUniq to remove PCR duplicates from my trimmed and paired sequencing reads (150 BP PE done on the Illumina HiSeq X).

I first created an input file:

ls site1_R1_P.fq site1_R2_P.fq > site1_input.txt

Everything looks fine:

$ cat site1_input.txt
site1_R1_P.fq 
site1_R2_P.fq

But I am getting the error: "Error in open left fastq file site1_R1_P_qtrim.fq for read!"

I searched through the previous questions that relate to this error but the resolutions to those don't seem to apply - ex. misplaced spaces in the input.txt file (made sure there is no spaces), unusual symbols (tried running without any underscores in case that counted as "unusual").

At a bit of a loss and I bet it's something silly so I appreciate any help!

Thank you!

[GenoMax]

If you have dos2unix command available on your machine just pass your input.txt file through it to ensure that line endings are proper.

[brenna.stanford1]

Thank you for the suggestion! I read through the material and will likely go that way.

Answer 1

[GenoMax]

Not a direct answer but I recommend that you use clumpify.sh from BBMap suite for this application (Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates. ). It will be fast, easy to use and will allow you to separate optical dups from PCR dups.

[brenna.stanford1]

Worked perfectly! Thank you.

Answer 2

[ChaiQ]

Maybe you can open your "site1_input.txt" with vim,if behind "site1_R1_P.fq" have space except "\n",please delete space and try again!