[2018-10-13 18:06:07] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:06:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:06:07] Checking for Bowtie index files (genome)..
[2018-10-13 18:06:07] Checking for reference FASTA file
[2018-10-13 18:06:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:06:13] Reading known junctions from GTF file
[2018-10-13 18:06:17] Preparing reads
	 left reads: min. length=100, max. length=100, 449447 kept reads (266 discarded)
	right reads: min. length=100, max. length=100, 448984 kept reads (729 discarded)
[2018-10-13 18:06:37] Building transcriptome data files /scratch/8793427.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:06:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:14:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:15:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:16:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:16:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:16:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:16:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:17:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:17:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:17:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:18:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:18:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:18:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:18:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:18:49] Searching for junctions via segment mapping
[2018-10-13 18:21:51] Retrieving sequences for splices
[2018-10-13 18:24:03] Indexing splices
[2018-10-13 18:24:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:24:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:24:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:24:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:24:42] Joining segment hits
[2018-10-13 18:27:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:27:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:27:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:27:23] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:27:28] Joining segment hits
[2018-10-13 18:29:51] Reporting output tracks
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[2018-10-13 18:33:44] A summary of the alignment counts can be found in /scratch/8793427.1.linga/tophat2/align_summary.txt
[2018-10-13 18:33:44] Run complete: 00:27:36 elapsed