[2018-10-13 15:55:14] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:55:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:55:14] Checking for Bowtie index files (genome)..
[2018-10-13 15:55:14] Checking for reference FASTA file
[2018-10-13 15:55:14] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:55:19] Reading known junctions from GTF file
[2018-10-13 15:55:23] Preparing reads
	 left reads: min. length=100, max. length=100, 844641 kept reads (279 discarded)
	right reads: min. length=100, max. length=100, 844081 kept reads (839 discarded)
[2018-10-13 15:56:00] Building transcriptome data files /scratch/8793334.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:56:21] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:05:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:06:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:07:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:07:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:08:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:08:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:08:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:09:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:09:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:10:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:10:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:10:46] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:11:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:11:13] Searching for junctions via segment mapping
[2018-10-13 16:14:24] Retrieving sequences for splices
[2018-10-13 16:16:35] Indexing splices
[2018-10-13 16:16:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:17:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:17:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:17:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:17:16] Joining segment hits
[2018-10-13 16:19:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:20:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:20:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:20:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:20:16] Joining segment hits
[2018-10-13 16:22:49] Reporting output tracks
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[2018-10-13 16:28:00] A summary of the alignment counts can be found in /scratch/8793334.1.linga/tophat2/align_summary.txt
[2018-10-13 16:28:00] Run complete: 00:32:45 elapsed