[2018-10-13 00:06:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:06:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:06:44] Checking for Bowtie index files (genome)..
[2018-10-13 00:06:44] Checking for reference FASTA file
[2018-10-13 00:06:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:06:49] Reading known junctions from GTF file
[2018-10-13 00:06:53] Preparing reads
	 left reads: min. length=100, max. length=100, 240503 kept reads (124 discarded)
	right reads: min. length=100, max. length=100, 240270 kept reads (357 discarded)
[2018-10-13 00:07:05] Building transcriptome data files /scratch/8792856.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:07:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:16:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:16:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:17:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:17:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:17:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:17:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:18:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:18:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:18:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:18:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:18:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:19:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:19:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:19:28] Searching for junctions via segment mapping
[2018-10-13 00:22:06] Retrieving sequences for splices
[2018-10-13 00:24:18] Indexing splices
[2018-10-13 00:24:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:24:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:24:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:24:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:24:57] Joining segment hits
[2018-10-13 00:27:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:27:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:27:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:27:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:27:32] Joining segment hits
[2018-10-13 00:29:52] Reporting output tracks
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[2018-10-13 00:33:20] A summary of the alignment counts can be found in /scratch/8792856.1.linga/tophat2/align_summary.txt
[2018-10-13 00:33:20] Run complete: 00:26:35 elapsed