[2018-10-12 21:58:13] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:58:13] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:58:13] Checking for Bowtie index files (genome)..
[2018-10-12 21:58:13] Checking for reference FASTA file
[2018-10-12 21:58:13] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:58:18] Reading known junctions from GTF file
[2018-10-12 21:58:23] Preparing reads
	 left reads: min. length=100, max. length=100, 358033 kept reads (182 discarded)
	right reads: min. length=100, max. length=100, 357743 kept reads (472 discarded)
[2018-10-12 21:58:39] Building transcriptome data files /scratch/8792774.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:59:01] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:07:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:08:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:08:42] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:08:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:09:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:09:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:09:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:09:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:10:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:10:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:11:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:11:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:11:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:11:35] Searching for junctions via segment mapping
[2018-10-12 22:14:35] Retrieving sequences for splices
[2018-10-12 22:16:53] Indexing splices
[2018-10-12 22:17:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:17:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:17:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:17:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:17:32] Joining segment hits
[2018-10-12 22:20:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:20:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:20:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:20:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:20:21] Joining segment hits
[2018-10-12 22:22:52] Reporting output tracks
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[2018-10-12 22:26:30] A summary of the alignment counts can be found in /scratch/8792774.1.linga/tophat2/align_summary.txt
[2018-10-12 22:26:30] Run complete: 00:28:16 elapsed