[2018-10-13 00:11:43] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:11:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:11:43] Checking for Bowtie index files (genome)..
[2018-10-13 00:11:43] Checking for reference FASTA file
[2018-10-13 00:11:43] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:11:47] Reading known junctions from GTF file
[2018-10-13 00:11:52] Preparing reads
	 left reads: min. length=100, max. length=100, 421903 kept reads (294 discarded)
	right reads: min. length=100, max. length=100, 421495 kept reads (702 discarded)
[2018-10-13 00:12:13] Building transcriptome data files /scratch/8792858.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:12:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:21:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:22:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:22:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:22:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:23:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:23:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:23:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:24:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:24:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:24:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:25:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:25:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:25:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:25:32] Searching for junctions via segment mapping
[2018-10-13 00:28:26] Retrieving sequences for splices
[2018-10-13 00:30:42] Indexing splices
[2018-10-13 00:31:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:31:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:31:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:31:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:31:22] Joining segment hits
[2018-10-13 00:33:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:33:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:33:59] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:34:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:34:07] Joining segment hits
[2018-10-13 00:36:38] Reporting output tracks
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[2018-10-13 00:40:51] A summary of the alignment counts can be found in /scratch/8792858.1.linga/tophat2/align_summary.txt
[2018-10-13 00:40:51] Run complete: 00:29:08 elapsed