[2019-06-18 11:07:54] Beginning TopHat run (v2.1.1)
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[2019-06-18 11:07:54] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-18 11:07:54] Checking for Bowtie index files (genome)..
[2019-06-18 11:07:54] Checking for reference FASTA file
[2019-06-18 11:07:54] Generating SAM header for Bowtie2Index/genome
[2019-06-18 11:08:01] Reading known junctions from GTF file
[2019-06-18 11:08:06] Preparing reads
	 left reads: min. length=50, max. length=50, 58576091 kept reads (181607 discarded)
	right reads: min. length=50, max. length=50, 58390974 kept reads (366724 discarded)
[2019-06-18 11:35:31] Building transcriptome data files /scratch/6794467.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-18 11:35:52] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-18 11:43:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:00:40] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:18:07] Resuming TopHat pipeline with unmapped reads
[2019-06-18 12:18:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 12:47:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 12:52:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:01:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 13:32:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 13:38:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:50:15] Searching for junctions via segment mapping
[2019-06-18 14:01:09] Retrieving sequences for splices
[2019-06-18 14:03:43] Indexing splices
[2019-06-18 14:04:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 14:04:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 14:05:37] Joining segment hits
[2019-06-18 14:10:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 14:11:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 14:12:20] Joining segment hits
[2019-06-18 14:17:23] Reporting output tracks
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[2019-06-18 15:20:23] A summary of the alignment counts can be found in /scratch/6794467.1.linga/tophat2/align_summary.txt
[2019-06-18 15:20:23] Run complete: 04:12:28 elapsed