[2018-10-13 07:53:35] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:53:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:53:35] Checking for Bowtie index files (genome)..
[2018-10-13 07:53:35] Checking for reference FASTA file
[2018-10-13 07:53:35] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:53:39] Reading known junctions from GTF file
[2018-10-13 07:53:43] Preparing reads
	 left reads: min. length=100, max. length=100, 752352 kept reads (58 discarded)
	right reads: min. length=100, max. length=100, 752133 kept reads (277 discarded)
[2018-10-13 07:54:09] Building transcriptome data files /scratch/8793098.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:54:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:01:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:02:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:02:50] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:02:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:03:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:03:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:03:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:03:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:04:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:04:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:04:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:04:54] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:05:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:05:14] Searching for junctions via segment mapping
[2018-10-13 08:08:09] Retrieving sequences for splices
[2018-10-13 08:10:07] Indexing splices
[2018-10-13 08:10:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:10:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:10:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:10:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:10:43] Joining segment hits
[2018-10-13 08:12:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:12:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:12:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:13:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:13:06] Joining segment hits
[2018-10-13 08:15:13] Reporting output tracks
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[2018-10-13 08:19:11] A summary of the alignment counts can be found in /scratch/8793098.1.linga/tophat2/align_summary.txt
[2018-10-13 08:19:11] Run complete: 00:25:36 elapsed