[2018-10-13 02:28:36] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:28:36] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:28:36] Checking for Bowtie index files (genome)..
[2018-10-13 02:28:36] Checking for reference FASTA file
[2018-10-13 02:28:36] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:28:40] Reading known junctions from GTF file
[2018-10-13 02:28:44] Preparing reads
	 left reads: min. length=100, max. length=100, 480651 kept reads (295 discarded)
	right reads: min. length=100, max. length=100, 480369 kept reads (577 discarded)
[2018-10-13 02:29:06] Building transcriptome data files /scratch/8792918.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:29:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:37:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:38:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:39:31] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:39:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:40:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:40:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:40:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:41:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:41:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:42:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:42:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:42:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:42:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:42:49] Searching for junctions via segment mapping
[2018-10-13 02:45:42] Retrieving sequences for splices
[2018-10-13 02:47:51] Indexing splices
[2018-10-13 02:48:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:48:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:48:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:48:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:48:30] Joining segment hits
[2018-10-13 02:51:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:51:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:51:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:51:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:51:36] Joining segment hits
[2018-10-13 02:54:07] Reporting output tracks
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[2018-10-13 02:58:06] A summary of the alignment counts can be found in /scratch/8792918.1.linga/tophat2/align_summary.txt
[2018-10-13 02:58:06] Run complete: 00:29:30 elapsed