[2018-10-13 07:27:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:27:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:27:29] Checking for Bowtie index files (genome)..
[2018-10-13 07:27:29] Checking for reference FASTA file
[2018-10-13 07:27:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:27:33] Reading known junctions from GTF file
[2018-10-13 07:27:38] Preparing reads
	 left reads: min. length=100, max. length=100, 765649 kept reads (95 discarded)
	right reads: min. length=100, max. length=100, 765401 kept reads (343 discarded)
[2018-10-13 07:28:07] Building transcriptome data files /scratch/8793087.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:28:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:36:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:37:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:39:29] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:39:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:40:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:40:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:40:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:40:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:40:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:41:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:41:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:41:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:41:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:42:02] Searching for junctions via segment mapping
[2018-10-13 07:47:56] Retrieving sequences for splices
[2018-10-13 07:50:08] Indexing splices
[2018-10-13 07:50:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:50:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:50:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:50:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:51:03] Joining segment hits
[2018-10-13 07:53:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:53:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:53:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:53:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:54:00] Joining segment hits
[2018-10-13 07:56:32] Reporting output tracks
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[2018-10-13 08:16:32] A summary of the alignment counts can be found in /scratch/8793087.1.linga/tophat2/align_summary.txt
[2018-10-13 08:16:32] Run complete: 00:49:02 elapsed