[2018-10-13 03:26:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:26:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:26:30] Checking for Bowtie index files (genome)..
[2018-10-13 03:26:30] Checking for reference FASTA file
[2018-10-13 03:26:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:26:34] Reading known junctions from GTF file
[2018-10-13 03:26:38] Preparing reads
	 left reads: min. length=100, max. length=100, 372455 kept reads (271 discarded)
	right reads: min. length=100, max. length=100, 372210 kept reads (516 discarded)
[2018-10-13 03:26:55] Building transcriptome data files /scratch/8792957.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:27:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:36:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:36:40] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:37:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:37:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:38:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:38:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:38:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:38:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:38:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:39:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:39:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:39:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:40:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:40:10] Searching for junctions via segment mapping
[2018-10-13 03:42:53] Retrieving sequences for splices
[2018-10-13 03:45:02] Indexing splices
[2018-10-13 03:45:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:45:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:45:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:45:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:45:41] Joining segment hits
[2018-10-13 03:48:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:48:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:48:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:48:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:48:35] Joining segment hits
[2018-10-13 03:51:05] Reporting output tracks
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[2018-10-13 03:54:39] A summary of the alignment counts can be found in /scratch/8792957.1.linga/tophat2/align_summary.txt
[2018-10-13 03:54:39] Run complete: 00:28:09 elapsed