[2018-10-13 10:04:07] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:04:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:04:07] Checking for Bowtie index files (genome)..
[2018-10-13 10:04:07] Checking for reference FASTA file
[2018-10-13 10:04:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:04:11] Reading known junctions from GTF file
[2018-10-13 10:04:15] Preparing reads
	 left reads: min. length=100, max. length=100, 1622023 kept reads (96 discarded)
	right reads: min. length=100, max. length=100, 1621338 kept reads (781 discarded)
[2018-10-13 10:05:24] Building transcriptome data files /scratch/8793166.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:05:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:13:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:14:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:16:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:16:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:16:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:16:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:17:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:17:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:17:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:18:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:18:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:18:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:18:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:19:01] Searching for junctions via segment mapping
[2018-10-13 10:23:14] Retrieving sequences for splices
[2018-10-13 10:25:17] Indexing splices
[2018-10-13 10:25:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:25:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:25:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:26:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:26:09] Joining segment hits
[2018-10-13 10:28:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:28:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:28:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:29:04] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:29:11] Joining segment hits
[2018-10-13 10:31:40] Reporting output tracks
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[2018-10-13 10:45:21] A summary of the alignment counts can be found in /scratch/8793166.1.linga/tophat2/align_summary.txt
[2018-10-13 10:45:21] Run complete: 00:41:14 elapsed