[2018-10-13 15:24:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:24:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:24:05] Checking for Bowtie index files (genome)..
[2018-10-13 15:24:05] Checking for reference FASTA file
[2018-10-13 15:24:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:24:10] Reading known junctions from GTF file
[2018-10-13 15:24:15] Preparing reads
	 left reads: min. length=100, max. length=100, 675988 kept reads (256 discarded)
	right reads: min. length=100, max. length=100, 675543 kept reads (701 discarded)
[2018-10-13 15:24:46] Building transcriptome data files /scratch/8793316.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:25:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:33:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:34:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:34:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:34:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:35:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:35:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:35:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:36:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:36:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:36:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:36:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:37:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:37:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:37:28] Searching for junctions via segment mapping
[2018-10-13 15:41:20] Retrieving sequences for splices
[2018-10-13 15:43:19] Indexing splices
[2018-10-13 15:43:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:43:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:43:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:43:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:44:01] Joining segment hits
[2018-10-13 15:47:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:47:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:47:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:47:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:47:36] Joining segment hits
[2018-10-13 15:49:55] Reporting output tracks
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[2018-10-13 15:57:49] A summary of the alignment counts can be found in /scratch/8793316.1.linga/tophat2/align_summary.txt
[2018-10-13 15:57:49] Run complete: 00:33:43 elapsed