[2018-10-12 23:44:39] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:44:39] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:44:39] Checking for Bowtie index files (genome)..
[2018-10-12 23:44:39] Checking for reference FASTA file
[2018-10-12 23:44:39] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:44:45] Reading known junctions from GTF file
[2018-10-12 23:44:49] Preparing reads
	 left reads: min. length=100, max. length=100, 206864 kept reads (215 discarded)
	right reads: min. length=100, max. length=100, 206630 kept reads (449 discarded)
[2018-10-12 23:44:59] Building transcriptome data files /scratch/8792846.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:45:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:54:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:54:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:55:03] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:55:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:55:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:55:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:55:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:56:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:56:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:56:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:56:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:57:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:57:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:57:32] Searching for junctions via segment mapping
[2018-10-13 00:00:10] Retrieving sequences for splices
[2018-10-13 00:02:31] Indexing splices
[2018-10-13 00:02:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:02:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:03:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:03:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:03:10] Joining segment hits
[2018-10-13 00:05:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:05:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:05:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:05:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:06:03] Joining segment hits
[2018-10-13 00:08:30] Reporting output tracks
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[2018-10-13 00:11:37] A summary of the alignment counts can be found in /scratch/8792846.1.linga/tophat2/align_summary.txt
[2018-10-13 00:11:37] Run complete: 00:26:57 elapsed