[2018-10-13 16:50:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:50:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:50:15] Checking for Bowtie index files (genome)..
[2018-10-13 16:50:15] Checking for reference FASTA file
[2018-10-13 16:50:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:50:20] Reading known junctions from GTF file
[2018-10-13 16:50:24] Preparing reads
	 left reads: min. length=100, max. length=100, 621301 kept reads (404 discarded)
	right reads: min. length=100, max. length=100, 620886 kept reads (819 discarded)
[2018-10-13 16:50:49] Building transcriptome data files /scratch/8793373.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:51:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:59:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:00:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:01:07] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:01:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:01:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:02:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:02:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:02:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:02:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:03:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:03:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:03:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:04:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:04:13] Searching for junctions via segment mapping
[2018-10-13 17:07:08] Retrieving sequences for splices
[2018-10-13 17:09:13] Indexing splices
[2018-10-13 17:09:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:09:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:09:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:09:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:09:54] Joining segment hits
[2018-10-13 17:12:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:12:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:12:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:12:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:12:33] Joining segment hits
[2018-10-13 17:14:59] Reporting output tracks
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[2018-10-13 17:19:03] A summary of the alignment counts can be found in /scratch/8793373.1.linga/tophat2/align_summary.txt
[2018-10-13 17:19:03] Run complete: 00:28:47 elapsed