[2018-10-13 14:37:50] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:37:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:37:50] Checking for Bowtie index files (genome)..
[2018-10-13 14:37:50] Checking for reference FASTA file
[2018-10-13 14:37:50] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:37:54] Reading known junctions from GTF file
[2018-10-13 14:37:58] Preparing reads
	 left reads: min. length=100, max. length=100, 1698159 kept reads (106 discarded)
	right reads: min. length=100, max. length=100, 1697491 kept reads (774 discarded)
[2018-10-13 14:39:09] Building transcriptome data files /scratch/8793299.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:39:28] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:47:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:49:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:50:30] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:50:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:51:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:51:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:51:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:51:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:51:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:52:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:52:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:53:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:53:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:53:37] Searching for junctions via segment mapping
[2018-10-13 14:58:31] Retrieving sequences for splices
[2018-10-13 15:00:45] Indexing splices
[2018-10-13 15:01:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:01:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:01:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:01:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:01:37] Joining segment hits
[2018-10-13 15:04:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:04:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:04:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:04:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:04:34] Joining segment hits
[2018-10-13 15:07:42] Reporting output tracks
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[2018-10-13 15:24:25] A summary of the alignment counts can be found in /scratch/8793299.1.linga/tophat2/align_summary.txt
[2018-10-13 15:24:25] Run complete: 00:46:34 elapsed