[2018-10-13 17:35:59] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:35:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:35:59] Checking for Bowtie index files (genome)..
[2018-10-13 17:35:59] Checking for reference FASTA file
[2018-10-13 17:35:59] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:36:04] Reading known junctions from GTF file
[2018-10-13 17:36:08] Preparing reads
	 left reads: min. length=100, max. length=100, 114293 kept reads (185 discarded)
	right reads: min. length=100, max. length=100, 114180 kept reads (298 discarded)
[2018-10-13 17:36:14] Building transcriptome data files /scratch/8793405.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:36:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:44:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:45:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:45:20] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:45:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:45:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:45:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:45:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:46:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:46:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:46:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:46:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:46:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:47:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:47:10] Searching for junctions via segment mapping
[2018-10-13 17:49:32] Retrieving sequences for splices
[2018-10-13 17:51:47] Indexing splices
[2018-10-13 17:52:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:52:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:52:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:52:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:52:21] Joining segment hits
[2018-10-13 17:54:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:54:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:54:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:55:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:55:07] Joining segment hits
[2018-10-13 17:57:26] Reporting output tracks
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[2018-10-13 17:59:56] A summary of the alignment counts can be found in /scratch/8793405.1.linga/tophat2/align_summary.txt
[2018-10-13 17:59:56] Run complete: 00:23:57 elapsed