[2018-10-13 11:06:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:06:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:06:03] Checking for Bowtie index files (genome)..
[2018-10-13 11:06:03] Checking for reference FASTA file
[2018-10-13 11:06:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:06:08] Reading known junctions from GTF file
[2018-10-13 11:06:12] Preparing reads
	 left reads: min. length=100, max. length=100, 1084920 kept reads (95 discarded)
	right reads: min. length=100, max. length=100, 1084612 kept reads (403 discarded)
[2018-10-13 11:06:59] Building transcriptome data files /scratch/8793193.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:07:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:15:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:16:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:17:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:17:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:17:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:17:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:18:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:18:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:18:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:19:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:19:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:19:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:19:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:20:04] Searching for junctions via segment mapping
[2018-10-13 11:23:37] Retrieving sequences for splices
[2018-10-13 11:25:43] Indexing splices
[2018-10-13 11:26:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:26:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:26:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:26:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:26:22] Joining segment hits
[2018-10-13 11:28:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:28:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:28:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:28:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:29:00] Joining segment hits
[2018-10-13 11:31:26] Reporting output tracks
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[2018-10-13 11:38:06] A summary of the alignment counts can be found in /scratch/8793193.1.linga/tophat2/align_summary.txt
[2018-10-13 11:38:06] Run complete: 00:32:02 elapsed