I have the same problem. My command is :
Code:
tophat -p 4 --genome-read-mismatches 3 --read-mismatches 3 --max-multihits 1 --b2-sensitive hg19 /home/darstr/tmp/ArrayStarProbes.fa
Code:
$ head /home/darstr/tmp/ArrayStarProbes.fa >CUST_385_PI426073487 ACTTGTTTCAGGTTAATGGTAAGAGTTACCCGCAGGCTAAGTTGCTATTGGGACAGATGG >ASHG19A3A032313 GAAACATCTTCCCAGAAAACAGACTACAACAAATCATTTCCCTGGTATGAAGGAATGAAG >ASHG19A3L0000337 AGATATCTGGTTGAGACCAAGTAAGAGATAAACCTGTAGATTCCACTGTGCCACCACAGT >ASHG19A3A014810 GGACAAGAATCCTTCAAAAAACAGGAAAAAACTCCTAAAACACCTAAAAGGACCTAGTTC >ASHG19A3A015967 AAGATCTTCATAGAAAGAGTCCAGGGGAACCCAACCCTATTGCACATCACAGATCTTCAG
Code:
$ samtools view -c tophat_out/accepted_hits.bam 0
I got the same 2 warning messages from my run as the original poster. I hope a new TopHat version is released soon.
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