[2018-10-13 06:37:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:37:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:37:41] Checking for Bowtie index files (genome)..
[2018-10-13 06:37:41] Checking for reference FASTA file
[2018-10-13 06:37:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:37:45] Reading known junctions from GTF file
[2018-10-13 06:37:49] Preparing reads
	 left reads: min. length=100, max. length=100, 1336351 kept reads (137 discarded)
	right reads: min. length=100, max. length=100, 1336062 kept reads (426 discarded)
[2018-10-13 06:38:44] Building transcriptome data files /scratch/8793059.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:39:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:47:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:49:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:51:55] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:51:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:52:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:53:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:53:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:53:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:54:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:55:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:55:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:55:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:56:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:56:16] Searching for junctions via segment mapping
[2018-10-13 07:05:43] Retrieving sequences for splices
[2018-10-13 07:08:00] Indexing splices
[2018-10-13 07:08:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:08:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:08:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:09:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:09:16] Joining segment hits
[2018-10-13 07:11:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:12:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:12:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:12:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:12:41] Joining segment hits
[2018-10-13 07:15:17] Reporting output tracks
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[2018-10-13 07:40:35] A summary of the alignment counts can be found in /scratch/8793059.1.linga/tophat2/align_summary.txt
[2018-10-13 07:40:35] Run complete: 01:02:54 elapsed