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SplitNCigarReads error on large genome with many scaffolds

rob123king2rob123king2 harpendenMember

At the SplitNCigarReads stag of the RNA-seq snp calling pipeline I get an error:

, v443_1408, v443_0446, v443_0426, v443_0764, v443_0561, v443_1760, v443_0086, v443_1056, v443_0286, v443_1519, v443_0153, v443_1436, v443_0415, v443_1158, v443_0766, v443_0700, v443_1681, v443_0178, v443_0217, v443_0525, v443_1599, v443_0673, v443_2778, v443_1121, v443_0406, v443_0468, v443_2680, v443_0344, v443_0447, v443_0378, v443_0931, Mt, v443_0510, v443_0690, v443_2777, v443_0792, v443_0628, v443_0172, v443_1826, v443_0676, v443_0003, v443_1540, v443_0934, v443_0708, v443_0135, v443_0549, v443_0484, v443_0872, v443_1547, v443_0919, v443_0974, v443_0403, v443_0858, v443_0577, v443_0056, 4D, 3D, 1D, 5A, 2D, 5D, 6D, 7A, 3A, 6B, 6A, 4A, 7D, 1A, 7B, 2A, 5B, 1B, 4B, 2B, 3B]

ERROR ------------------------------------------------------------------------------------------

Using below example with latest gatk 3.3:
java -Xmx20g -Djava.io.tmpdir=/home/data/tmp -jar ./GenomeAnalysisTK.jar -T SplitNCigarReads -R /home/data/IWGSC2.fasta -I rg_added_sorted.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

I'm guessing because the wheat genome is over 200,000 scaffolds that this is causing a problem? It doesn't appear to give any debugging information. Any ideas on a possible solution?

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