[2018-10-13 11:39:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:39:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:39:05] Checking for Bowtie index files (genome)..
[2018-10-13 11:39:05] Checking for reference FASTA file
[2018-10-13 11:39:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:39:10] Reading known junctions from GTF file
[2018-10-13 11:39:14] Preparing reads
	 left reads: min. length=100, max. length=100, 1053809 kept reads (59 discarded)
	right reads: min. length=100, max. length=100, 1053440 kept reads (428 discarded)
[2018-10-13 11:39:56] Building transcriptome data files /scratch/8793210.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:40:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:48:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:49:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:50:54] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:50:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:52:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:53:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:53:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:53:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:54:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:55:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:56:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:56:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:57:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:57:28] Searching for junctions via segment mapping
[2018-10-13 12:01:35] Retrieving sequences for splices
[2018-10-13 12:03:57] Indexing splices
[2018-10-13 12:04:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:04:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:04:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:04:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:04:46] Joining segment hits
[2018-10-13 12:07:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:07:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:07:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:08:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:08:06] Joining segment hits
[2018-10-13 12:10:52] Reporting output tracks
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[2018-10-13 12:19:14] A summary of the alignment counts can be found in /scratch/8793210.1.linga/tophat2/align_summary.txt
[2018-10-13 12:19:14] Run complete: 00:40:08 elapsed