[2018-10-12 22:49:19] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:49:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:49:19] Checking for Bowtie index files (genome)..
[2018-10-12 22:49:19] Checking for reference FASTA file
[2018-10-12 22:49:19] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:49:24] Reading known junctions from GTF file
[2018-10-12 22:49:28] Preparing reads
	 left reads: min. length=100, max. length=100, 377867 kept reads (103 discarded)
	right reads: min. length=100, max. length=100, 377702 kept reads (268 discarded)
[2018-10-12 22:49:47] Building transcriptome data files /scratch/8792812.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:50:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:58:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:58:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:59:15] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:59:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:59:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:00:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:00:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:00:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:00:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:01:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:01:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:01:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:01:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:01:53] Searching for junctions via segment mapping
[2018-10-12 23:04:35] Retrieving sequences for splices
[2018-10-12 23:06:55] Indexing splices
[2018-10-12 23:07:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:07:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:07:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:07:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:07:35] Joining segment hits
[2018-10-12 23:09:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:09:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:09:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:10:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:10:06] Joining segment hits
[2018-10-12 23:12:20] Reporting output tracks
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[2018-10-12 23:15:47] A summary of the alignment counts can be found in /scratch/8792812.1.linga/tophat2/align_summary.txt
[2018-10-12 23:15:47] Run complete: 00:26:28 elapsed