[2018-10-13 11:18:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:18:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:18:54] Checking for Bowtie index files (genome)..
[2018-10-13 11:18:54] Checking for reference FASTA file
[2018-10-13 11:18:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:18:57] Reading known junctions from GTF file
[2018-10-13 11:19:02] Preparing reads
	 left reads: min. length=100, max. length=100, 465806 kept reads (222 discarded)
	right reads: min. length=100, max. length=100, 465468 kept reads (560 discarded)
[2018-10-13 11:19:21] Building transcriptome data files /scratch/8793201.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:19:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:27:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:28:22] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:28:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:28:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:29:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:29:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:29:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:29:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:30:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:30:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:30:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:30:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:30:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:31:06] Searching for junctions via segment mapping
[2018-10-13 11:34:26] Retrieving sequences for splices
[2018-10-13 11:36:40] Indexing splices
[2018-10-13 11:36:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:37:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:37:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:37:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:37:17] Joining segment hits
[2018-10-13 11:40:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:40:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:40:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:40:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:40:50] Joining segment hits
[2018-10-13 11:43:20] Reporting output tracks
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[2018-10-13 11:47:57] A summary of the alignment counts can be found in /scratch/8793201.1.linga/tophat2/align_summary.txt
[2018-10-13 11:47:57] Run complete: 00:29:03 elapsed