[2018-10-13 13:20:18] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:20:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:20:18] Checking for Bowtie index files (genome)..
[2018-10-13 13:20:18] Checking for reference FASTA file
[2018-10-13 13:20:18] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:20:21] Reading known junctions from GTF file
[2018-10-13 13:20:23] Preparing reads
	 left reads: min. length=100, max. length=100, 1765715 kept reads (98 discarded)
	right reads: min. length=100, max. length=100, 1765129 kept reads (684 discarded)
[2018-10-13 13:21:08] Building transcriptome data files /scratch/8793259.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:21:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:25:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:26:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:27:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:27:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:27:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:28:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:28:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:28:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:28:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:28:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:29:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:29:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:29:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:29:37] Searching for junctions via segment mapping
[2018-10-13 13:32:23] Retrieving sequences for splices
[2018-10-13 13:34:15] Indexing splices
[2018-10-13 13:34:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:34:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:34:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:34:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:34:47] Joining segment hits
[2018-10-13 13:36:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:36:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:36:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:36:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:36:22] Joining segment hits
[2018-10-13 13:37:38] Reporting output tracks
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[2018-10-13 13:49:24] A summary of the alignment counts can be found in /scratch/8793259.1.linga/tophat2/align_summary.txt
[2018-10-13 13:49:24] Run complete: 00:29:05 elapsed