[2018-10-13 15:06:28] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:06:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:06:28] Checking for Bowtie index files (genome)..
[2018-10-13 15:06:28] Checking for reference FASTA file
[2018-10-13 15:06:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:06:32] Reading known junctions from GTF file
[2018-10-13 15:06:36] Preparing reads
	 left reads: min. length=100, max. length=100, 584406 kept reads (247 discarded)
	right reads: min. length=100, max. length=100, 584293 kept reads (360 discarded)
[2018-10-13 15:07:00] Building transcriptome data files /scratch/8793310.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:07:21] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:15:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:16:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:17:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:17:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:18:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:18:12] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:18:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:18:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:18:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:19:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:19:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:19:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:19:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:20:12] Searching for junctions via segment mapping
[2018-10-13 15:25:50] Retrieving sequences for splices
[2018-10-13 15:27:51] Indexing splices
[2018-10-13 15:28:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:28:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:28:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:28:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:28:39] Joining segment hits
[2018-10-13 15:31:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:31:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:31:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:31:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:31:35] Joining segment hits
[2018-10-13 15:34:24] Reporting output tracks
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[2018-10-13 15:50:39] A summary of the alignment counts can be found in /scratch/8793310.1.linga/tophat2/align_summary.txt
[2018-10-13 15:50:39] Run complete: 00:44:11 elapsed