'run_check' was not defined

[veronic...@gmail.com]

Hi,

Here is my command:" $JAFFA/tools/bin/bpipe run $JAFFA/JAFFA_direct.groovy $FASTQ"

I got the following error:
Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128
WARN: Error evaluating script /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/JAFFA-version-1.09/JAFFA_stages.groovy: No such property: bioinformatics for class: JAFFA_stages_bpipe
WARN: Error evaluating script /project/bioinformatics/Xiao_lab/s171162/fusionpro/software/JAFFA-version-1.09/JAFFA_stages.groovy: No such property: bioinformatics for class: JAFFA_stages_bpipe
====================================================================================================
| Starting Pipeline at 2018-03-08 11:40 |
====================================================================================================

Pipeline Failed!

A variable referred to in your script on line 20, 'run_check' was not defined.

Please check that all pipeline stages or other variables you have referenced by this name are defined.

I am really in need of your help!

Thanks.
Tianshi

[Nadia Davidson]

Hi Tianshi,

If you run the command with the full paths instead of using the variables $JAFFA and $FASTQ, does that work?

It looks like JAFFA can't find some of its files for some reason.

Cheers,

Nadia.

[veronic...@gmail.com]

Hi Nadia,

Thanks for your reply. I also have another problem. I am not able to download the reference files for hg38 and hg19 through this website: https://github.com/Oshlack/JAFFA/wiki/Download. Could you please place another link or kindly provide the files here?
I appreciate your help!

Thanks.
Tianshi

[veronic...@gmail.com]

Hi Nadia,

I found the download problem came from poor network connection. I got the reference files after the connection changed. 

Thanks,

Tianshi

[Nadia Davidson]

Great to hear.

[veronic...@gmail.com]

Hi Nadia,

Another problem came. My files are fastq files with names of A1_1.fastq and A1_2.fastq. I changed the 'fastqInputFormat=%_*.fastq.gz' to 'fastqInputFormat=%_*.fastq' in JAFFA_stages.groovy file.

It showed me the error  in Stage run_check that 'The pattern provided '%_*.fastq' did not match any of the files provided as input [checks]'.

Could you please help me figure it out?

Thanks,

Tianshi