[2018-10-13 11:18:49] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:18:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:18:49] Checking for Bowtie index files (genome)..
[2018-10-13 11:18:49] Checking for reference FASTA file
[2018-10-13 11:18:49] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:18:51] Reading known junctions from GTF file
[2018-10-13 11:18:53] Preparing reads
	 left reads: min. length=100, max. length=100, 1159208 kept reads (266 discarded)
	right reads: min. length=100, max. length=100, 1158920 kept reads (554 discarded)
[2018-10-13 11:19:25] Building transcriptome data files /scratch/8793202.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:19:35] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:24:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:25:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:26:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:26:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:27:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:27:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:27:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:27:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:28:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:28:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:28:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:28:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:28:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:29:07] Searching for junctions via segment mapping
[2018-10-13 11:34:36] Retrieving sequences for splices
[2018-10-13 11:35:43] Indexing splices
Building a SMALL index
[2018-10-13 11:35:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:36:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:36:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:36:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:36:19] Joining segment hits
[2018-10-13 11:37:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:37:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:37:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:37:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:38:01] Joining segment hits
[2018-10-13 11:39:20] Reporting output tracks
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[2018-10-13 11:53:22] A summary of the alignment counts can be found in /scratch/8793202.1.p8/tophat2/align_summary.txt
[2018-10-13 11:53:22] Run complete: 00:34:32 elapsed
[samopen] SAM header is present: 114 sequences.