[2018-10-13 06:12:36] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:12:36] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:12:36] Checking for Bowtie index files (genome)..
[2018-10-13 06:12:36] Checking for reference FASTA file
[2018-10-13 06:12:36] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:12:41] Reading known junctions from GTF file
[2018-10-13 06:12:46] Preparing reads
	 left reads: min. length=100, max. length=100, 711918 kept reads (115 discarded)
	right reads: min. length=100, max. length=100, 711563 kept reads (470 discarded)
[2018-10-13 06:13:16] Building transcriptome data files /scratch/8793048.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:13:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:22:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:23:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:23:53] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:23:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:24:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:24:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:24:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:24:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:25:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:25:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:25:43] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:25:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:26:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:26:22] Searching for junctions via segment mapping
[2018-10-13 06:31:03] Retrieving sequences for splices
[2018-10-13 06:33:07] Indexing splices
[2018-10-13 06:33:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:33:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:33:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:33:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:33:58] Joining segment hits
[2018-10-13 06:36:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:36:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:36:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:36:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:36:50] Joining segment hits
[2018-10-13 06:39:44] Reporting output tracks
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[2018-10-13 06:51:03] A summary of the alignment counts can be found in /scratch/8793048.1.linga/tophat2/align_summary.txt
[2018-10-13 06:51:03] Run complete: 00:38:27 elapsed