[2018-10-12 22:27:05] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:27:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:27:05] Checking for Bowtie index files (genome)..
[2018-10-12 22:27:05] Checking for reference FASTA file
[2018-10-12 22:27:05] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:27:07] Reading known junctions from GTF file
[2018-10-12 22:27:10] Preparing reads
	 left reads: min. length=100, max. length=100, 493311 kept reads (217 discarded)
	right reads: min. length=100, max. length=100, 492954 kept reads (574 discarded)
[2018-10-12 22:27:22] Building transcriptome data files /scratch/8792792.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:27:31] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:32:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:32:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:33:05] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:33:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:33:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:33:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:33:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:33:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:33:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:34:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:34:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:34:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:34:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:34:40] Searching for junctions via segment mapping
[2018-10-12 22:36:08] Retrieving sequences for splices
[2018-10-12 22:37:14] Indexing splices
[2018-10-12 22:37:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:37:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:37:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:37:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:37:34] Joining segment hits
[2018-10-12 22:38:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:38:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:38:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:38:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:39:01] Joining segment hits
[2018-10-12 22:40:18] Reporting output tracks
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[2018-10-12 22:42:26] A summary of the alignment counts can be found in /scratch/8792792.1.p16/tophat2/align_summary.txt
[2018-10-12 22:42:26] Run complete: 00:15:21 elapsed