[2018-10-13 11:28:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:28:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:28:29] Checking for Bowtie index files (genome)..
[2018-10-13 11:28:29] Checking for reference FASTA file
[2018-10-13 11:28:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:28:34] Reading known junctions from GTF file
[2018-10-13 11:28:38] Preparing reads
	 left reads: min. length=100, max. length=100, 481786 kept reads (238 discarded)
	right reads: min. length=100, max. length=100, 481318 kept reads (706 discarded)
[2018-10-13 11:29:00] Building transcriptome data files /scratch/8793205.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:29:21] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:38:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:38:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:39:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:39:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:39:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:39:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:40:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:40:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:40:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:41:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:41:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:41:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:41:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:41:43] Searching for junctions via segment mapping
[2018-10-13 11:44:54] Retrieving sequences for splices
[2018-10-13 11:47:02] Indexing splices
[2018-10-13 11:47:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:47:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:47:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:47:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:47:42] Joining segment hits
[2018-10-13 11:49:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:50:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:50:09] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:50:13] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:50:18] Joining segment hits
[2018-10-13 11:52:33] Reporting output tracks
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[2018-10-13 11:57:06] A summary of the alignment counts can be found in /scratch/8793205.1.linga/tophat2/align_summary.txt
[2018-10-13 11:57:06] Run complete: 00:28:37 elapsed