Originally posted by swbarnes2
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INPUT=s_3_2/s_3_2_unmap_genome.sam FASTQ=s_3_2/s_3_2_unmap_genome.fq VALIDATION_STRINGENCY=LENIENT Ignoring SAM validation error due to lenient parsing: Error parsing text SAM file. MAPQ should be 0 for unmapped read.; Line 3205583 Line: HWUSI-EAS724_0039:3:34:15714:3092#0 20 9 124595110 37 80M * 0 0 AGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAA ATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGG hggh]hghhhghghhhhhghhhhhhhhhhhdhhhhhhhcfhhghhhhhhhchhhghhfdhhhghhhhhhgghhghhghhh XT:A:U NM:i:1 XN :i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0G79
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