[2018-10-13 11:06:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:06:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:06:05] Checking for Bowtie index files (genome)..
[2018-10-13 11:06:05] Checking for reference FASTA file
[2018-10-13 11:06:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:06:11] Reading known junctions from GTF file
[2018-10-13 11:06:15] Preparing reads
	 left reads: min. length=100, max. length=100, 653857 kept reads (234 discarded)
	right reads: min. length=100, max. length=100, 653576 kept reads (515 discarded)
[2018-10-13 11:06:48] Building transcriptome data files /scratch/8793194.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:07:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:15:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:16:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:17:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:17:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:18:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:18:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:18:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:18:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:19:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:19:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:19:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:20:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:20:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:20:22] Searching for junctions via segment mapping
[2018-10-13 11:24:34] Retrieving sequences for splices
[2018-10-13 11:26:52] Indexing splices
[2018-10-13 11:27:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:27:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:27:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:27:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:27:35] Joining segment hits
[2018-10-13 11:30:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:30:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:30:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:30:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:30:25] Joining segment hits
[2018-10-13 11:33:05] Reporting output tracks
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[2018-10-13 11:39:24] A summary of the alignment counts can be found in /scratch/8793194.1.linga/tophat2/align_summary.txt
[2018-10-13 11:39:24] Run complete: 00:33:18 elapsed