[2018-10-13 17:54:59] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:54:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:54:59] Checking for Bowtie index files (genome)..
[2018-10-13 17:54:59] Checking for reference FASTA file
[2018-10-13 17:54:59] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:55:04] Reading known junctions from GTF file
[2018-10-13 17:55:08] Preparing reads
	 left reads: min. length=100, max. length=100, 221733 kept reads (344 discarded)
	right reads: min. length=100, max. length=100, 221753 kept reads (324 discarded)
[2018-10-13 17:55:19] Building transcriptome data files /scratch/8793415.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:55:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:03:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:04:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:04:54] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:04:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:05:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:05:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:05:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:05:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:05:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:06:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:06:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:06:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:06:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:07:00] Searching for junctions via segment mapping
[2018-10-13 18:09:36] Retrieving sequences for splices
[2018-10-13 18:12:11] Indexing splices
[2018-10-13 18:12:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:12:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:12:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:12:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:12:52] Joining segment hits
[2018-10-13 18:15:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:15:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:15:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:15:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:15:41] Joining segment hits
[2018-10-13 18:18:02] Reporting output tracks
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[2018-10-13 18:21:12] A summary of the alignment counts can be found in /scratch/8793415.1.linga/tophat2/align_summary.txt
[2018-10-13 18:21:12] Run complete: 00:26:13 elapsed