[2018-10-13 06:17:50] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:17:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:17:50] Checking for Bowtie index files (genome)..
[2018-10-13 06:17:50] Checking for reference FASTA file
[2018-10-13 06:17:50] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:17:54] Reading known junctions from GTF file
[2018-10-13 06:17:58] Preparing reads
	 left reads: min. length=100, max. length=100, 923869 kept reads (93 discarded)
	right reads: min. length=100, max. length=100, 923656 kept reads (306 discarded)
[2018-10-13 06:18:38] Building transcriptome data files /scratch/8793052.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:18:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:26:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:27:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:28:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:28:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:29:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:29:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:29:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:29:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:29:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:30:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:30:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:30:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:31:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:31:16] Searching for junctions via segment mapping
[2018-10-13 06:35:32] Retrieving sequences for splices
[2018-10-13 06:37:44] Indexing splices
[2018-10-13 06:38:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:38:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:38:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:38:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:38:32] Joining segment hits
[2018-10-13 06:41:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:41:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:41:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:41:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:41:34] Joining segment hits
[2018-10-13 06:44:04] Reporting output tracks
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[2018-10-13 06:54:09] A summary of the alignment counts can be found in /scratch/8793052.1.linga/tophat2/align_summary.txt
[2018-10-13 06:54:09] Run complete: 00:36:18 elapsed