[2018-10-13 03:17:02] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:17:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:17:03] Checking for Bowtie index files (genome)..
[2018-10-13 03:17:03] Checking for reference FASTA file
[2018-10-13 03:17:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:17:07] Reading known junctions from GTF file
[2018-10-13 03:17:12] Preparing reads
	 left reads: min. length=100, max. length=100, 386051 kept reads (326 discarded)
	right reads: min. length=100, max. length=100, 385715 kept reads (662 discarded)
[2018-10-13 03:17:27] Building transcriptome data files /scratch/8792954.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:17:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:25:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:26:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:27:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:27:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:27:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:27:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:28:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:28:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:28:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:29:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:29:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:29:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:29:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:30:01] Searching for junctions via segment mapping
[2018-10-13 03:32:41] Retrieving sequences for splices
[2018-10-13 03:34:47] Indexing splices
[2018-10-13 03:35:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:35:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:35:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:35:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:35:23] Joining segment hits
[2018-10-13 03:37:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:37:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:37:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:37:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:37:50] Joining segment hits
[2018-10-13 03:40:00] Reporting output tracks
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[2018-10-13 03:43:21] A summary of the alignment counts can be found in /scratch/8792954.1.linga/tophat2/align_summary.txt
[2018-10-13 03:43:21] Run complete: 00:26:18 elapsed