[2018-10-13 17:48:02] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:48:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:48:02] Checking for Bowtie index files (genome)..
[2018-10-13 17:48:02] Checking for reference FASTA file
[2018-10-13 17:48:02] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:48:06] Reading known junctions from GTF file
[2018-10-13 17:48:10] Preparing reads
	 left reads: min. length=100, max. length=100, 525019 kept reads (448 discarded)
	right reads: min. length=100, max. length=100, 525093 kept reads (374 discarded)
[2018-10-13 17:48:34] Building transcriptome data files /scratch/8793411.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:48:54] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:56:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:57:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:58:15] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:58:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:58:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:58:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:59:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:59:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:59:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:00:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:00:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:00:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:00:36] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:00:47] Searching for junctions via segment mapping
[2018-10-13 18:03:49] Retrieving sequences for splices
[2018-10-13 18:05:59] Indexing splices
[2018-10-13 18:06:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:06:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:06:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:06:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:06:40] Joining segment hits
[2018-10-13 18:09:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:09:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:09:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:09:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:09:26] Joining segment hits
[2018-10-13 18:11:48] Reporting output tracks
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[2018-10-13 18:16:00] A summary of the alignment counts can be found in /scratch/8793411.1.linga/tophat2/align_summary.txt
[2018-10-13 18:16:00] Run complete: 00:27:58 elapsed