[2018-10-13 12:24:27] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:24:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:24:27] Checking for Bowtie index files (genome)..
[2018-10-13 12:24:27] Checking for reference FASTA file
[2018-10-13 12:24:27] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:24:32] Reading known junctions from GTF file
[2018-10-13 12:24:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1087567 kept reads (155 discarded)
	right reads: min. length=100, max. length=100, 1087202 kept reads (520 discarded)
[2018-10-13 12:25:22] Building transcriptome data files /scratch/8793230.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:25:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:34:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:35:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:36:33] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:36:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:37:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:37:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:37:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:37:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:37:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:38:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:38:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:38:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:39:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:39:22] Searching for junctions via segment mapping
[2018-10-13 12:44:10] Retrieving sequences for splices
[2018-10-13 12:46:24] Indexing splices
[2018-10-13 12:46:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:46:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:47:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:47:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:47:16] Joining segment hits
[2018-10-13 12:50:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:50:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:50:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:50:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:50:37] Joining segment hits
[2018-10-13 12:53:12] Reporting output tracks
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[2018-10-13 13:05:57] A summary of the alignment counts can be found in /scratch/8793230.1.linga/tophat2/align_summary.txt
[2018-10-13 13:05:57] Run complete: 00:41:29 elapsed