[2018-10-13 12:53:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:53:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:53:51] Checking for Bowtie index files (genome)..
[2018-10-13 12:53:51] Checking for reference FASTA file
[2018-10-13 12:53:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:53:54] Reading known junctions from GTF file
[2018-10-13 12:53:57] Preparing reads
	 left reads: min. length=100, max. length=100, 793495 kept reads (230 discarded)
	right reads: min. length=100, max. length=100, 793287 kept reads (438 discarded)
[2018-10-13 12:54:20] Building transcriptome data files /scratch/8793245.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:54:31] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:59:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:59:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:00:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:00:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:00:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:00:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:00:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:00:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:01:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:01:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:01:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:01:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:02:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:02:07] Searching for junctions via segment mapping
[2018-10-13 13:05:05] Retrieving sequences for splices
[2018-10-13 13:06:09] Indexing splices
[2018-10-13 13:06:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:06:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:06:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:06:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:06:41] Joining segment hits
[2018-10-13 13:07:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:08:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:08:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:08:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:08:15] Joining segment hits
[2018-10-13 13:09:29] Reporting output tracks
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[2018-10-13 13:13:29] A summary of the alignment counts can be found in /scratch/8793245.1.linga/tophat2/align_summary.txt
[2018-10-13 13:13:29] Run complete: 00:19:37 elapsed