[2018-10-13 11:59:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:59:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:59:58] Checking for Bowtie index files (genome)..
[2018-10-13 11:59:58] Checking for reference FASTA file
[2018-10-13 11:59:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:00:03] Reading known junctions from GTF file
[2018-10-13 12:00:09] Preparing reads
	 left reads: min. length=100, max. length=100, 575083 kept reads (133 discarded)
	right reads: min. length=100, max. length=100, 574947 kept reads (269 discarded)
[2018-10-13 12:00:36] Building transcriptome data files /scratch/8793223.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:00:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:09:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:11:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:13:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:13:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:14:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:14:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:15:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:15:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:15:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:16:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:16:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:16:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:16:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:17:06] Searching for junctions via segment mapping
[2018-10-13 12:26:08] Retrieving sequences for splices
[2018-10-13 12:28:39] Indexing splices
[2018-10-13 12:29:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:29:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:29:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:29:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:29:58] Joining segment hits
[2018-10-13 12:32:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:32:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:33:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:33:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:33:24] Joining segment hits
[2018-10-13 12:36:10] Reporting output tracks
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[2018-10-13 13:06:18] A summary of the alignment counts can be found in /scratch/8793223.1.linga/tophat2/align_summary.txt
[2018-10-13 13:06:18] Run complete: 01:06:20 elapsed