[2018-10-13 00:14:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:14:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:14:57] Checking for Bowtie index files (genome)..
[2018-10-13 00:14:57] Checking for reference FASTA file
[2018-10-13 00:14:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:15:02] Reading known junctions from GTF file
[2018-10-13 00:15:07] Preparing reads
	 left reads: min. length=100, max. length=100, 428476 kept reads (215 discarded)
	right reads: min. length=100, max. length=100, 428219 kept reads (472 discarded)
[2018-10-13 00:15:28] Building transcriptome data files /scratch/8792860.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:15:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:24:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:25:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:25:50] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:25:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:26:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:26:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:27:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:27:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:27:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:28:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:28:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:28:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:28:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:28:59] Searching for junctions via segment mapping
[2018-10-13 00:31:46] Retrieving sequences for splices
[2018-10-13 00:33:56] Indexing splices
[2018-10-13 00:34:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:34:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:34:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:34:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:34:32] Joining segment hits
[2018-10-13 00:36:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:36:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:36:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:36:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:37:04] Joining segment hits
[2018-10-13 00:39:16] Reporting output tracks
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[2018-10-13 00:43:08] A summary of the alignment counts can be found in /scratch/8792860.1.linga/tophat2/align_summary.txt
[2018-10-13 00:43:08] Run complete: 00:28:11 elapsed