[2018-10-13 17:28:00] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:28:00] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:28:00] Checking for Bowtie index files (genome)..
[2018-10-13 17:28:00] Checking for reference FASTA file
[2018-10-13 17:28:00] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:28:04] Reading known junctions from GTF file
[2018-10-13 17:28:08] Preparing reads
	 left reads: min. length=100, max. length=100, 266727 kept reads (303 discarded)
	right reads: min. length=100, max. length=100, 266547 kept reads (483 discarded)
[2018-10-13 17:28:19] Building transcriptome data files /scratch/8793397.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:28:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:36:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:36:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:37:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:37:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:37:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:38:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:38:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:38:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:38:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:39:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:39:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:39:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:39:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:39:49] Searching for junctions via segment mapping
[2018-10-13 17:43:05] Retrieving sequences for splices
[2018-10-13 17:45:17] Indexing splices
[2018-10-13 17:45:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:45:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:45:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:45:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:45:56] Joining segment hits
[2018-10-13 17:48:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:48:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:48:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:48:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:48:47] Joining segment hits
[2018-10-13 17:51:22] Reporting output tracks
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[2018-10-13 17:55:02] A summary of the alignment counts can be found in /scratch/8793397.1.linga/tophat2/align_summary.txt
[2018-10-13 17:55:02] Run complete: 00:27:02 elapsed