[2018-10-13 14:24:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:24:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:24:32] Checking for Bowtie index files (genome)..
[2018-10-13 14:24:32] Checking for reference FASTA file
[2018-10-13 14:24:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:24:36] Reading known junctions from GTF file
[2018-10-13 14:24:40] Preparing reads
	 left reads: min. length=100, max. length=100, 1480405 kept reads (123 discarded)
	right reads: min. length=100, max. length=100, 1479814 kept reads (714 discarded)
[2018-10-13 14:25:40] Building transcriptome data files /scratch/8793288.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:25:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:33:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:34:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:35:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:35:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:36:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:36:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:36:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:36:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:36:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:37:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:37:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:37:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:38:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:38:20] Searching for junctions via segment mapping
[2018-10-13 14:42:23] Retrieving sequences for splices
[2018-10-13 14:44:29] Indexing splices
[2018-10-13 14:44:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:44:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:45:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:45:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:45:16] Joining segment hits
[2018-10-13 14:47:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:47:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:47:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:48:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:48:07] Joining segment hits
[2018-10-13 14:50:35] Reporting output tracks
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[2018-10-13 15:01:52] A summary of the alignment counts can be found in /scratch/8793288.1.linga/tophat2/align_summary.txt
[2018-10-13 15:01:52] Run complete: 00:37:20 elapsed