[2018-10-13 12:37:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:37:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:37:10] Checking for Bowtie index files (genome)..
[2018-10-13 12:37:10] Checking for reference FASTA file
[2018-10-13 12:37:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:37:15] Reading known junctions from GTF file
[2018-10-13 12:37:19] Preparing reads
	 left reads: min. length=100, max. length=100, 1483627 kept reads (93 discarded)
	right reads: min. length=100, max. length=100, 1483222 kept reads (498 discarded)
[2018-10-13 12:38:25] Building transcriptome data files /scratch/8793240.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:38:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:48:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:49:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:51:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:51:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:52:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:52:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:52:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:53:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:53:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:54:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:54:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:54:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:54:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:54:56] Searching for junctions via segment mapping
[2018-10-13 13:00:54] Retrieving sequences for splices
[2018-10-13 13:03:06] Indexing splices
[2018-10-13 13:03:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:03:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:03:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:03:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:04:06] Joining segment hits
[2018-10-13 13:06:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:06:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:06:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:07:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:07:16] Joining segment hits
[2018-10-13 13:10:13] Reporting output tracks
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[2018-10-13 13:29:30] A summary of the alignment counts can be found in /scratch/8793240.1.linga/tophat2/align_summary.txt
[2018-10-13 13:29:30] Run complete: 00:52:20 elapsed