[2018-10-12 22:01:57] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:01:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:01:57] Checking for Bowtie index files (genome)..
[2018-10-12 22:01:57] Checking for reference FASTA file
[2018-10-12 22:01:57] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:02:01] Reading known junctions from GTF file
[2018-10-12 22:02:06] Preparing reads
	 left reads: min. length=100, max. length=100, 320716 kept reads (227 discarded)
	right reads: min. length=100, max. length=100, 320459 kept reads (484 discarded)
[2018-10-12 22:02:20] Building transcriptome data files /scratch/8792777.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:02:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:10:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:11:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:05] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:12:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:12:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:12:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:13:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:13:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:13:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:14:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:14:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:14:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:14:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:14:50] Searching for junctions via segment mapping
[2018-10-12 22:17:23] Retrieving sequences for splices
[2018-10-12 22:19:29] Indexing splices
[2018-10-12 22:19:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:19:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:19:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:20:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:20:05] Joining segment hits
[2018-10-12 22:22:22] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:22:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:22:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:22:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:22:39] Joining segment hits
[2018-10-12 22:24:52] Reporting output tracks
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[2018-10-12 22:28:12] A summary of the alignment counts can be found in /scratch/8792777.1.linga/tophat2/align_summary.txt
[2018-10-12 22:28:12] Run complete: 00:26:15 elapsed