[2018-10-13 01:48:25] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:48:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:48:25] Checking for Bowtie index files (genome)..
[2018-10-13 01:48:25] Checking for reference FASTA file
[2018-10-13 01:48:25] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:48:34] Reading known junctions from GTF file
[2018-10-13 01:48:39] Preparing reads
	 left reads: min. length=100, max. length=100, 264076 kept reads (171 discarded)
	right reads: min. length=100, max. length=100, 263814 kept reads (433 discarded)
[2018-10-13 01:48:53] Building transcriptome data files /scratch/8792897.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:49:15] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:58:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:59:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:59:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:59:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:00:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:00:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:00:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:00:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:01:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:01:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:01:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:02:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:02:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:02:28] Searching for junctions via segment mapping
[2018-10-13 02:05:10] Retrieving sequences for splices
[2018-10-13 02:07:23] Indexing splices
[2018-10-13 02:07:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:07:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:07:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:07:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:08:02] Joining segment hits
[2018-10-13 02:10:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:10:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:10:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:10:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:10:40] Joining segment hits
[2018-10-13 02:13:00] Reporting output tracks
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[2018-10-13 02:16:22] A summary of the alignment counts can be found in /scratch/8792897.1.linga/tophat2/align_summary.txt
[2018-10-13 02:16:22] Run complete: 00:27:56 elapsed