started new star analysis

dge_workflow/star_align.sh

@@ -107,15 +107,21 @@ for fastqFile in $fastqFiles ; do
     # --quantMode GeneCounts see https://groups.google.com/forum/#!searchin/rna-star/GeneCounts/rna-star/gZRJx3ElRNo/p5FjBYKuY00J
     # --outSJfilterCountUniqueMin see https://groups.google.com/forum/#!topic/rna-star/_1BeAlGUmpA
 
-    mysub "${project}__star__${fastqBaseName}" "
+    jl submit -j .starjobs -q medium -t 5 -n "${project}__star__${fastqBaseName}" "
     STAR --genomeDir $star_index --readFilesIn $fastqFile --runThreadN 6 --readFilesCommand zcat --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile $gtfFile --outFilterIntronMotifs   RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3
     mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
     samtools index ${fastqBaseName}.bam
-    " -n 5 -R span[hosts=1] -q medium | joblist .starjobs
+    "
 done
 
 
-wait4jobs .starjobs
+jl wait .starjobs
+
+if [ -n "$(jl failed .starjobs)" ]; then
+    echo "some jobs failed"; exit 1
+fi
+
+jl status --report .starjobs
 
 
 rm -rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out