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YeoLab / gscripts

General Use Scripts and Helper functions
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Errors Running RNA-Seq pipeline for paired end samples #63

Closed shassathe closed 9 years ago

shassathe commented 9 years ago

I get the following bunch of errors while executing rna-seq pipeline for paired end samples:

INFO 10:27:34,813 QScriptManager - Compiling 1 QScript ERROR 10:27:38,149 QScriptManager - analyze_rna_seq.scala:243: noAdapterFastq is already defined as value noAdapterFastq ERROR 10:27:38,164 QScriptManager - val noAdapterFastq = swapExt(noGzFastq, ".fastq", ".polyATrim.adapterTrim.fastq") ERROR 10:27:38,164 QScriptManager - ^ ERROR 10:27:38,164 QScriptManager - analyze_rna_seq.scala:246: filteredFastq is already defined as value filteredFastq ERROR 10:27:38,167 QScriptManager - val filteredFastq = swapExt(outRep, "", "Unmapped.out.mate1") ERROR 10:27:38,167 QScriptManager - ^ ERROR 10:27:38,167 QScriptManager - analyze_rna_seq.scala:247: adapterReport is already defined as value adapterReport ERROR 10:27:38,168 QScriptManager - val adapterReport = swapExt(noAdapterFastq, ".fastq", ".metrics") ERROR 10:27:38,168 QScriptManager - ^ ERROR 10:27:38,169 QScriptManager - analyze_rna_seq.scala:224: not found: value <<<<<<< ERROR 10:27:38,170 QScriptManager - <<<<<<< HEAD ERROR 10:27:38,171 QScriptManager - ^ ERROR 10:27:38,214 QScriptManager - analyze_rna_seq.scala:241: not found: value ======= ERROR 10:27:38,215 QScriptManager - ======= ERROR 10:27:38,217 QScriptManager - ^ ERROR 10:27:38,229 QScriptManager - analyze_rna_seq.scala:266: not found: value >>>>>>> ERROR 10:27:38,230 QScriptManager - >>>>>>> a9363b5262030453d45d4e0150e5932d52220e3b ERROR 10:27:38,230 QScriptManager - ^ ERROR 10:27:38,277 QScriptManager - analyze_rna_seq.scala:298: not enough arguments for method apply: (fastqFile: AnalyzeRNASeq.this.File, fastqPair: AnalyzeRNASeq.this.File, adapter: List[String], dummy: AnalyzeRNASeq.this.File, isPaired: Boolean)AnalyzeRNASeq.this.trimGalore in object trimGalore. Unspecified value parameters dummy, isPaired. ERROR 10:27:38,278 QScriptManager - add(trimGalore(fastqFile = fastqFile, fastqPair=fastqPair, adapter = adapter)) ERROR 10:27:38,278 QScriptManager - ^ ERROR 10:27:38,463 QScriptManager - analyze_rna_seq.scala:441: filteredFastq is already defined as variable filteredFastq ERROR 10:27:38,463 QScriptManager - val (filteredFastq, filteredPair) = stringentJobs(fastqFile, fastqPair) ERROR 10:27:38,464 QScriptManager - ^ ERROR 10:27:38,468 QScriptManager - analyze_rna_seq.scala:400: not found: value <<<<<<< ERROR 10:27:38,469 QScriptManager - <<<<<<< HEAD ERROR 10:27:38,469 QScriptManager - ^ ERROR 10:27:38,482 QScriptManager - analyze_rna_seq.scala:418: reassignment to val ERROR 10:27:38,482 QScriptManager - filteredFastq = filteredFiles._1 ERROR 10:27:38,483 QScriptManager - ^ ERROR 10:27:38,484 QScriptManager - analyze_rna_seq.scala:421: reassignment to val ERROR 10:27:38,484 QScriptManager - filteredFastq = fastqFile ERROR 10:27:38,485 QScriptManager - ^ ERROR 10:27:38,492 QScriptManager - analyze_rna_seq.scala:428: reassignment to val ERROR 10:27:38,493 QScriptManager - filteredFastq = filteredFiles._1 ERROR 10:27:38,493 QScriptManager - ^ ERROR 10:27:38,494 QScriptManager - analyze_rna_seq.scala:430: reassignment to val ERROR 10:27:38,494 QScriptManager - filteredFastq = stringentJobs(fastqFile) ERROR 10:27:38,495 QScriptManager - ^ ERROR 10:27:38,495 QScriptManager - analyze_rna_seq.scala:433: reassignment to val ERROR 10:27:38,496 QScriptManager - filteredFastq = fastqFile ERROR 10:27:38,496 QScriptManager - ^ ERROR 10:27:38,497 QScriptManager - analyze_rna_seq.scala:436: not found: value ======= ERROR 10:27:38,498 QScriptManager - ======= ERROR 10:27:38,498 QScriptManager - ^ ERROR 10:27:38,500 QScriptManager - analyze_rna_seq.scala:443: not found: value >>>>>>> ERROR 10:27:38,501 QScriptManager - >>>>>>> a9363b5262030453d45d4e0150e5932d52220e3b ERROR 10:27:38,501 QScriptManager - ^ ERROR 10:27:38,897 QScriptManager - 16 errors found

olgabot commented 9 years ago

This is because the files were merged improperly. I was the last to touch this file so it was probably me

olgabot commented 9 years ago

oh wait no I wasn't... in any case. Shashank, you have an old version with merge conflicts. This is the newest version: https://github.com/YeoLab/gscripts/blob/master/qscripts/analyze_rna_seq.scala and there's no merge conflicts there. To force check out the latest master, do:

cd ~/gscripts
git fetch
git checkout origin master   

# The "checkout" command will complain that you're in a "DETACHED HEAD STATE"
# To fix that, do a pull:
git pull origin master