[2018-10-13 06:54:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:54:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:54:40] Checking for Bowtie index files (genome)..
[2018-10-13 06:54:40] Checking for reference FASTA file
[2018-10-13 06:54:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:54:44] Reading known junctions from GTF file
[2018-10-13 06:54:48] Preparing reads
	 left reads: min. length=100, max. length=100, 97632 kept reads (189 discarded)
	right reads: min. length=100, max. length=100, 97506 kept reads (315 discarded)
[2018-10-13 06:54:53] Building transcriptome data files /scratch/8793069.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:55:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:03:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:03:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:04:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:04:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:04:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:04:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:04:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:04:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:04:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:05:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:05:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:05:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:05:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:05:50] Searching for junctions via segment mapping
[2018-10-13 07:08:11] Retrieving sequences for splices
[2018-10-13 07:10:19] Indexing splices
[2018-10-13 07:10:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:10:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:10:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:10:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:10:55] Joining segment hits
[2018-10-13 07:13:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:13:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:13:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:13:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:13:24] Joining segment hits
[2018-10-13 07:15:43] Reporting output tracks
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[2018-10-13 07:18:16] A summary of the alignment counts can be found in /scratch/8793069.1.linga/tophat2/align_summary.txt
[2018-10-13 07:18:16] Run complete: 00:23:36 elapsed