error in trim

[wittney-m]

Hi I received an error message when I ran the following code:

IRFinder -m FastQ -r /home/analysis/REF/ -d ${f}_irfinder ${f}_R1_001_trim.fastq ${f}_R1.fastq

The output reads:

ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. WARN: ERROR: The paired-end trimming routine appeared not to have completed. It may have crashed if there was corruption in the input fastq files. Do the input fastq files have the same number of lines?

I ran the trim my fastq files. Why am I getting this output?

[dg520]

@wittney-m You might misunderstand the command.
IRFinder -m FastQ will run all the three steps of 1) fastq trimming; 2) alignment to the reference; and 3) IR quantification. It is NOT just to trim the reads. And you should provide untrimmed reads to it.
I will assume that 1) your library is paired-end; and 2) you have successfully prepared the IRFinder reference and saved it at /home/analysis/REF. Then it correct commend to run is:

IRFinder -m FastQ -r /home/analysis/REF/ -d ${f}_irfinder ${f}_R1.fastq ${f}_R2.fastq

[wittney-m]

Thank you. I ran the code that you provided but I am still getting this error:

ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. ERROR: IRFinder appears not to have completed. It appears an unknown component crashed.

I have attached the log. Log.out.txt

[dg520]

@wittney-m OK. In addition to the wrong command configuration, which has been solve now, the compiled IRFinder core that comes with the package is not compatible with your machine. You need to re-compile it via your local GCC and GLIBC. See here how to achieve it.