[2018-10-13 07:21:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:21:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:21:56] Checking for Bowtie index files (genome)..
[2018-10-13 07:21:56] Checking for reference FASTA file
[2018-10-13 07:21:56] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:22:01] Reading known junctions from GTF file
[2018-10-13 07:22:05] Preparing reads
	 left reads: min. length=100, max. length=100, 596662 kept reads (192 discarded)
	right reads: min. length=100, max. length=100, 596532 kept reads (322 discarded)
[2018-10-13 07:22:32] Building transcriptome data files /scratch/8793083.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:22:52] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:31:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:31:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:32:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:32:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:33:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:33:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:33:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:33:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:33:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:34:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:34:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:34:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:34:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:34:55] Searching for junctions via segment mapping
[2018-10-13 07:38:29] Retrieving sequences for splices
[2018-10-13 07:40:36] Indexing splices
[2018-10-13 07:40:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:41:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:41:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:41:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:41:18] Joining segment hits
[2018-10-13 07:43:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:43:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:43:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:43:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:44:05] Joining segment hits
[2018-10-13 07:46:28] Reporting output tracks
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[2018-10-13 07:52:52] A summary of the alignment counts can be found in /scratch/8793083.1.linga/tophat2/align_summary.txt
[2018-10-13 07:52:52] Run complete: 00:30:55 elapsed