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YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
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analyze_clip_seq.scala error #81

Closed broughtonjp closed 8 years ago

broughtonjp commented 8 years ago

I'm getting this error when running analyze_clip_seq.scala:

INFO  13:40:25,093 QScriptManager - Compiling 1 QScript
ERROR 13:40:30,017 QScriptManager - analyze_clip_seq.scala:283: type mismatch;
 found   : ((AnalizeCLIPSeq.this.File, String, String, String, String, String, String)) => Unit
 required: ((java.io.File, String, String, String, String, String)) => ?
ERROR 13:40:30,023 QScriptManager -       for (item : Tuple7[File, String, String, String, String, String, String] <- valueList) {
ERROR 13:40:30,023 QScriptManager -                                                                                ^
ERROR 13:40:30,156 QScriptManager - one error found
INFO  13:40:30,283 QCommandLine - Shutting down jobs. Please wait...
Nodes:        tscc-1-53

My gscripts and gatk are up-to-date. Any thoughts on how I can fix this? Thanks.

gpratt commented 8 years ago

Double check its up to date. This error indicates either gatk or gscripts is out of date. I may have forgotten to push the latest update. I'm away from my laptop right now, I'll check in a few hours. On Nov 19, 2015 2:21 PM, "James Broughton" notifications@github.com wrote:

I'm getting this error when running analyze_clip_seq.scala:

INFO 13:40:25,093 QScriptManager - Compiling 1 QScript ERROR 13:40:30,017 QScriptManager - analyze_clip_seq.scala:283: type mismatch; found : ((AnalizeCLIPSeq.this.File, String, String, String, String, String, String)) => Unit required: ((java.io.File, String, String, String, String, String)) => ? ERROR 13:40:30,023 QScriptManager - for (item : Tuple7[File, String, String, String, String, String, String] <- valueList) { ERROR 13:40:30,023 QScriptManager - ^ ERROR 13:40:30,156 QScriptManager - one error found INFO 13:40:30,283 QCommandLine - Shutting down jobs. Please wait... Nodes: tscc-1-53

My gscripts and gatk are up-to-date. Any thoughts on how I can fix this? Thanks.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/81.

broughtonjp commented 8 years ago

Yep, everything's up to date on my end.

gpratt commented 8 years ago

Send me the command so I can repo it. On Nov 19, 2015 2:36 PM, "James Broughton" notifications@github.com wrote:

Yep, everything's up to date on my end.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/81#issuecomment-158222686.

broughtonjp commented 8 years ago

qsub /home/jbrought/scratch/iclip/scripts/run_clipper.v2.sh

broughtonjp commented 8 years ago

Did these updates get pushed?

gpratt commented 8 years ago

Thanks for the reminder, pushed.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Mon, Nov 23, 2015 at 10:17 AM, James Broughton notifications@github.com wrote:

Did these updates get pushed?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/81#issuecomment-159017275.