[2018-10-13 14:17:01] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:17:01] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:17:01] Checking for Bowtie index files (genome)..
[2018-10-13 14:17:01] Checking for reference FASTA file
[2018-10-13 14:17:01] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:17:05] Reading known junctions from GTF file
[2018-10-13 14:17:09] Preparing reads
	 left reads: min. length=100, max. length=100, 474748 kept reads (231 discarded)
	right reads: min. length=100, max. length=100, 474388 kept reads (591 discarded)
[2018-10-13 14:17:31] Building transcriptome data files /scratch/8793283.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:17:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:25:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:26:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:27:15] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:27:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:27:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:27:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:28:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:28:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:28:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:28:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:29:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:29:17] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:29:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:29:39] Searching for junctions via segment mapping
[2018-10-13 14:33:55] Retrieving sequences for splices
[2018-10-13 14:36:02] Indexing splices
[2018-10-13 14:36:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:36:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:36:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:36:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:36:46] Joining segment hits
[2018-10-13 14:39:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:39:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:39:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:39:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:39:35] Joining segment hits
[2018-10-13 14:42:03] Reporting output tracks
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[2018-10-13 14:50:20] A summary of the alignment counts can be found in /scratch/8793283.1.linga/tophat2/align_summary.txt
[2018-10-13 14:50:20] Run complete: 00:33:19 elapsed