[2018-10-12 23:38:06] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:38:06] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:38:06] Checking for Bowtie index files (genome)..
[2018-10-12 23:38:06] Checking for reference FASTA file
[2018-10-12 23:38:06] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:38:10] Reading known junctions from GTF file
[2018-10-12 23:38:14] Preparing reads
	 left reads: min. length=100, max. length=100, 3311627 kept reads (1014 discarded)
	right reads: min. length=100, max. length=100, 3310999 kept reads (1642 discarded)
[2018-10-12 23:40:28] Building transcriptome data files /scratch/8792845.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:40:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:49:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:54:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:59:08] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:59:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:01:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:01:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:02:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:03:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:04:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:06:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:06:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:07:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:08:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:09:27] Searching for junctions via segment mapping
[2018-10-13 00:27:48] Retrieving sequences for splices
[2018-10-13 00:29:58] Indexing splices
[2018-10-13 00:30:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:30:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:31:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:31:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:32:23] Joining segment hits
[2018-10-13 00:35:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:35:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:36:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:37:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:37:41] Joining segment hits
[2018-10-13 00:40:38] Reporting output tracks
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[2018-10-13 01:50:25] A summary of the alignment counts can be found in /scratch/8792845.1.linga/tophat2/align_summary.txt
[2018-10-13 01:50:25] Run complete: 02:12:19 elapsed