error running ChIA-PET2 pipeline: trimLinker tool not found

Question

[alemagli]

Hi all, I'm trying to use the ChIA-PET2 pipeline but, after installation, it does not run and give me the error: trimLinker tool not found. Following the instructions, the ChIA-PET2 pipeline was installed in the bin directory, which contains all the tools from the package (including trimLinker). I attempted to run trimLinker by itself and it worked fine (or at least I think so). After that I used the readout of trimLinker to run ChIA-PET2 starting from step 2 ( using -s 2) and again it did not work.

Has anybody successfully used this package? I am not very experienced and any help will be very appreciated.

Best regards, Alessandro

Answer 1

[guipeng.lee]

The ChIA-PET2 pipeline will be installed in ~/bin/ChIA-PET2_version/bin by default. It's recommended to set this path to the PATH environment variable. I tested it again and it works fine in my case. Below is some output info.

~/bin/ChIA-PET2_0.9.2/bin/ChIA-PET2 -g ~/hg19/hg19.fa -b ~/hg19/hg19.chrom.sizes -f SRR525042_1.fastq -r SRR525042_2.fastq -o tttt -n test

[06-09 10:03:54] Start ChIA-PET2 V0.9.2 ...

[06-09 10:03:54] Running Step 1: Trim Linker ...

trimLinker -t 1 -m 0 -k 0 -e 0 -l 15 -o tttt -n test -A GTTGGATAAG -B GTTGGAATGT SRR525042_1.fastq SRR525042_2.fastq thread is 1 mode is 0 keepempty is 0 Error allowed is 0 min length of trimmed read is 15 Output dir is tttt Output name is test linkerA is GTTGGATAAG linkerB is GTTGGAATGT Reads 1: SRR525042_1.fastq Reads 2: SRR525042_2.fastq Processed 2000000 pair reads Processed 2000000 pair reads Processed 2000000 pair reads