[2018-10-13 14:27:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:27:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:27:34] Checking for Bowtie index files (genome)..
[2018-10-13 14:27:34] Checking for reference FASTA file
[2018-10-13 14:27:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:27:39] Reading known junctions from GTF file
[2018-10-13 14:27:43] Preparing reads
	 left reads: min. length=100, max. length=100, 337436 kept reads (85 discarded)
	right reads: min. length=100, max. length=100, 336913 kept reads (608 discarded)
[2018-10-13 14:27:57] Building transcriptome data files /scratch/8793290.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:28:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:36:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:36:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:37:17] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:37:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:37:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:37:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:37:59] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:38:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:38:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:38:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:38:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:39:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:39:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:39:19] Searching for junctions via segment mapping
[2018-10-13 14:42:15] Retrieving sequences for splices
[2018-10-13 14:44:21] Indexing splices
[2018-10-13 14:44:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:44:45] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:44:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:44:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:44:58] Joining segment hits
[2018-10-13 14:47:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:47:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:47:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:47:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:47:45] Joining segment hits
[2018-10-13 14:50:02] Reporting output tracks
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[2018-10-13 14:53:51] A summary of the alignment counts can be found in /scratch/8793290.1.linga/tophat2/align_summary.txt
[2018-10-13 14:53:51] Run complete: 00:26:17 elapsed