[2018-10-13 03:56:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:56:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:56:16] Checking for Bowtie index files (genome)..
[2018-10-13 03:56:16] Checking for reference FASTA file
[2018-10-13 03:56:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:56:21] Reading known junctions from GTF file
[2018-10-13 03:56:25] Preparing reads
	 left reads: min. length=100, max. length=100, 1081929 kept reads (87 discarded)
	right reads: min. length=100, max. length=100, 1081700 kept reads (316 discarded)
[2018-10-13 03:57:12] Building transcriptome data files /scratch/8792978.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:57:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:06:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:07:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:09:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:09:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:09:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:09:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:10:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:10:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:10:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:11:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:11:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:11:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:11:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:12:03] Searching for junctions via segment mapping
[2018-10-13 04:16:48] Retrieving sequences for splices
[2018-10-13 04:19:00] Indexing splices
[2018-10-13 04:19:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:19:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:19:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:19:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:19:52] Joining segment hits
[2018-10-13 04:22:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:22:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:22:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:22:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:22:53] Joining segment hits
[2018-10-13 04:25:28] Reporting output tracks
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[2018-10-13 04:39:41] A summary of the alignment counts can be found in /scratch/8792978.1.linga/tophat2/align_summary.txt
[2018-10-13 04:39:41] Run complete: 00:43:24 elapsed