search

YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
18 stars 18 forks source link

Type mismatch in analyze_rna_seq.scala #74

Closed olgabot closed 8 years ago

olgabot commented 9 years ago

Seems like some argument list didn't get updated in either the upstream GATK or this gscripts scala file.

Error:

[obotvinnik@tscc-2-48 scripts]$ sh 20150609_ys_rbfox2kd_v1.sh
INFO  07:21:47,795 QScriptManager - Compiling 1 QScript 
ERROR 07:21:54,638 QScriptManager - analyze_rna_seq.scala:295: type mismatch;
 found   : ((AnalyzeRNASeq.this.File, String, String, String, String, String)) => Unit
 required: ((java.io.File, String, String)) => ? 
ERROR 07:21:54,661 QScriptManager -       for (item: Tuple6[File, String, String, String, String, String] <- valueList) { 
ERROR 07:21:54,661 QScriptManager -                                                                       ^ 
ERROR 07:21:55,619 QScriptManager - one error found 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.queue.QException: Compile of /home/obotvinnik/gscripts/qscripts/analyze_rna_seq.scala failed with 1 error
        at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:71)
        at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95)
        at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:227)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:202)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-1148-g6dfb8a8):
##### ERROR
##### ERROR Please check the documentation guide to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Compile of /home/obotvinnik/gscripts/qscripts/analyze_rna_seq.scala failed with 1 error
##### ERROR ------------------------------------------------------------------------------------------
INFO  07:21:55,716 QCommandLine - Shutting down jobs. Please wait...

Script file:

#!/bin/bash

NAME=20150609_ys_rbfox2kd
VERSION=v1
DIR=20150609_ys_rbfox2kd
java -Xms512m -Xmx512m -jar ~/workspace-git/gatk/dist/Queue.jar -S $HOME/gscripts/qscripts/analyze_rna_seq.scala --input ${NAME}_${VERSION}.txt --adapter TCGTATGCCGTCTTCTGCTTG --adapter ATCTCGTATGCCGTCTTCTGCTTG --adapter CGACAGGTTCAGAGTTCTACAGTCCGACGATC --adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -qsub -jobQueue home-scrm -runDir ~/projects/${DIR}/analysis/${NAME}_${VERSION}  -log ${NAME}_${VERSION}.log --location ${NAME}  --strict -keepIntermediates --not_stranded -single_end -run

Manifest:

/home/obotvinnik/scratch/projects/20150609_ys_rbfox2kd/data/AD023_GAGTGG_L001_R1.fastq.gz       hg19
/home/obotvinnik/scratch/projects/20150609_ys_rbfox2kd/data/AD010_TAGCTT_L001_R1.fastq.gz       hg19
/home/obotvinnik/scratch/projects/20150609_ys_rbfox2kd/data/AD027_ATTCCT_L001_R1.fastq.gz       hg19
/home/obotvinnik/scratch/projects/20150609_ys_rbfox2kd/data/AD025_ACTGAT_L001_R1.fastq.gz       hg19

Using latest gscripts master, Last 3 commits in gscripts via git log:

commit 5230cbf41ac8d588c3a2ee8b2413315b6f6e7ecc
Merge: ab6b7e5 61c12ee
Author: Gabriel Pratt <gpratt@ucsd.edu>
Date:   Mon Jun 22 12:54:22 2015 -0700

    Merge branch 'master' of github.com:YeoLab/gscripts

commit ab6b7e58de637215f78e47512cf78b03e5451c35
Author: Gabriel Pratt <gpratt@ucsd.edu>
Date:   Mon Jun 22 12:53:56 2015 -0700

    updated analysis scripts to use Tuple6 for the manifest, to allow for more barcode commands

commit 61c12ee0de96acaecf6d6a5706d538bcfc2bea41
Author: Olga Botvinnik <olga.botvinnik@gmail.com>
Date:   Thu Jun 18 14:18:24 2015 -0700

    always make project folder in ~/projects

Using latest gpratt/gatk for gatk. git log from gatk directory:

commit 6dfb8a813d0c15d52039440982cfe5db4976e5c8
Author: Gabriel Pratt <gpratt@ucsd.edu>
Date:   Tue May 5 16:12:49 2015 -0700

    updated walltimes

commit 905c06ac33a34a36e0b40930987f4460a8464bf7
Merge: 762c1b4 fdd5e27
Author: Gabriel Pratt <gabriel.pratt@gmail.com>
Date:   Mon Mar 9 10:11:01 2015 -0700

    Merge pull request #11 from olgabot/trim_galore

    Add trim_galore for trimming paired-end reads and bowtie2 for mapping to repetitive regions
olgabot commented 9 years ago

The error is here: https://github.com/YeoLab/gscripts/blob/master/qscripts/analyze_rna_seq.scala#L295

Seems like it has somethign to do with the new Tuple6 thing, which in the last commit said it was necessary to have more barcode options

gpratt commented 9 years ago

Did you update queue itself? On Jun 25, 2015 8:40 AM, "Olga Botvinnik" notifications@github.com wrote:

The error is here: https://github.com/YeoLab/gscripts/blob/master/qscripts/analyze_rna_seq.scala#L295

Seems like it has somethign to do with the new Tuple6 thing, which in the last commit said it was necessary to have more barcode options

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115298191.

olgabot commented 9 years ago

I did a git pull upstream master on GATK - is that what you mean?

gpratt commented 9 years ago

Did you re-compile gatk?

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

On Thu, Jun 25, 2015 at 10:51 AM, Olga Botvinnik notifications@github.com wrote:

I did a git pull upstream master on GATK - is that what you mean?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115343377.

olgabot commented 9 years ago

yeah reupdated and recopiled

On Thu, Jun 25, 2015 at 11:16 AM Gabriel Pratt notifications@github.com wrote:

Did you re-compile gatk?

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

On Thu, Jun 25, 2015 at 10:51 AM, Olga Botvinnik <notifications@github.com

wrote:

I did a git pull upstream master on GATK - is that what you mean?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115343377.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115351855.

gpratt commented 9 years ago

and it still doesn't work?

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

On Thu, Jun 25, 2015 at 2:13 PM, Olga Botvinnik notifications@github.com wrote:

yeah reupdated and recopiled

On Thu, Jun 25, 2015 at 11:16 AM Gabriel Pratt notifications@github.com wrote:

Did you re-compile gatk?

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

On Thu, Jun 25, 2015 at 10:51 AM, Olga Botvinnik < notifications@github.com

wrote:

I did a git pull upstream master on GATK - is that what you mean?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115343377.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115351855.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/74#issuecomment-115399838.