[2018-10-13 09:58:21] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:58:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:58:21] Checking for Bowtie index files (genome)..
[2018-10-13 09:58:21] Checking for reference FASTA file
[2018-10-13 09:58:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:58:25] Reading known junctions from GTF file
[2018-10-13 09:58:29] Preparing reads
	 left reads: min. length=100, max. length=100, 1267246 kept reads (115 discarded)
	right reads: min. length=100, max. length=100, 1266760 kept reads (601 discarded)
[2018-10-13 09:59:17] Building transcriptome data files /scratch/8793161.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:59:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:06:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:07:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:08:33] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:08:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:09:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:09:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:09:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:09:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:09:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:10:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:10:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:10:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:10:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:11:03] Searching for junctions via segment mapping
[2018-10-13 10:15:08] Retrieving sequences for splices
[2018-10-13 10:17:09] Indexing splices
[2018-10-13 10:17:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:17:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:17:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:17:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:17:54] Joining segment hits
[2018-10-13 10:20:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:20:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:20:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:20:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:21:03] Joining segment hits
[2018-10-13 10:23:24] Reporting output tracks
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[2018-10-13 10:33:08] A summary of the alignment counts can be found in /scratch/8793161.1.linga/tophat2/align_summary.txt
[2018-10-13 10:33:08] Run complete: 00:34:47 elapsed