[2018-10-13 10:04:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:04:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:04:09] Checking for Bowtie index files (genome)..
[2018-10-13 10:04:09] Checking for reference FASTA file
[2018-10-13 10:04:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:04:14] Reading known junctions from GTF file
[2018-10-13 10:04:19] Preparing reads
	 left reads: min. length=100, max. length=100, 2154479 kept reads (1519 discarded)
	right reads: min. length=100, max. length=100, 2153912 kept reads (2086 discarded)
[2018-10-13 10:05:43] Building transcriptome data files /scratch/8793165.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:06:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:14:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:17:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:21:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:21:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:22:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:23:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:24:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:24:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:25:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:27:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:27:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:28:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:29:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:30:03] Searching for junctions via segment mapping
[2018-10-13 10:47:11] Retrieving sequences for splices
[2018-10-13 10:49:36] Indexing splices
[2018-10-13 10:49:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:50:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:50:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:50:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:51:20] Joining segment hits
[2018-10-13 10:53:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:54:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:54:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:55:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:55:25] Joining segment hits
[2018-10-13 10:58:10] Reporting output tracks
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[2018-10-13 11:42:43] A summary of the alignment counts can be found in /scratch/8793165.1.linga/tophat2/align_summary.txt
[2018-10-13 11:42:43] Run complete: 01:38:33 elapsed