[2018-10-13 13:28:54] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:28:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:28:54] Checking for Bowtie index files (genome)..
[2018-10-13 13:28:54] Checking for reference FASTA file
[2018-10-13 13:28:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:28:58] Reading known junctions from GTF file
[2018-10-13 13:29:02] Preparing reads
	 left reads: min. length=100, max. length=100, 795830 kept reads (61 discarded)
	right reads: min. length=100, max. length=100, 795551 kept reads (340 discarded)
[2018-10-13 13:29:35] Building transcriptome data files /scratch/8793261.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:29:55] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:37:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:39:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:40:13] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:40:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:40:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:40:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:41:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:41:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:41:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:41:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:41:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:42:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:42:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:42:30] Searching for junctions via segment mapping
[2018-10-13 13:47:30] Retrieving sequences for splices
[2018-10-13 13:49:40] Indexing splices
[2018-10-13 13:50:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:50:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:50:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:50:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:50:30] Joining segment hits
[2018-10-13 13:52:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:52:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:53:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:53:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:53:17] Joining segment hits
[2018-10-13 13:55:38] Reporting output tracks
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[2018-10-13 14:12:24] A summary of the alignment counts can be found in /scratch/8793261.1.linga/tophat2/align_summary.txt
[2018-10-13 14:12:24] Run complete: 00:43:29 elapsed