[2018-10-13 06:49:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:49:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:49:10] Checking for Bowtie index files (genome)..
[2018-10-13 06:49:10] Checking for reference FASTA file
[2018-10-13 06:49:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:49:14] Reading known junctions from GTF file
[2018-10-13 06:49:18] Preparing reads
	 left reads: min. length=100, max. length=100, 948783 kept reads (89 discarded)
	right reads: min. length=100, max. length=100, 948501 kept reads (371 discarded)
[2018-10-13 06:49:57] Building transcriptome data files /scratch/8793066.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:50:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:58:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:59:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:00:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:00:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:00:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:01:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:01:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:01:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:01:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:02:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:02:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:02:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:02:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:02:59] Searching for junctions via segment mapping
[2018-10-13 07:06:14] Retrieving sequences for splices
[2018-10-13 07:08:13] Indexing splices
[2018-10-13 07:08:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:08:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:08:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:08:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:08:51] Joining segment hits
[2018-10-13 07:11:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:11:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:11:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:11:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:11:27] Joining segment hits
[2018-10-13 07:13:43] Reporting output tracks
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[2018-10-13 07:18:41] A summary of the alignment counts can be found in /scratch/8793066.1.linga/tophat2/align_summary.txt
[2018-10-13 07:18:41] Run complete: 00:29:31 elapsed