[2019-07-17 22:28:26] Beginning TopHat run (v2.1.1)
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[2019-07-17 22:28:26] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 22:28:27] Checking for Bowtie index files (genome)..
[2019-07-17 22:28:27] Checking for reference FASTA file
[2019-07-17 22:28:27] Generating SAM header for Bowtie2Index/genome
[2019-07-17 22:28:31] Reading known junctions from GTF file
[2019-07-17 22:28:34] Preparing reads
	 left reads: min. length=101, max. length=101, 16396908 kept reads (579 discarded)
	right reads: min. length=101, max. length=101, 16389792 kept reads (7695 discarded)
[2019-07-17 22:53:51] Building transcriptome data files /scratch/7776706.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 22:54:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 23:00:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 23:25:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 23:37:38] Resuming TopHat pipeline with unmapped reads
[2019-07-17 23:37:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 23:52:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-07-17 23:54:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-07-17 23:56:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-07-17 23:58:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-07-18 00:01:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 00:09:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-07-18 00:10:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-07-18 00:11:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-07-18 00:13:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-07-18 00:14:43] Searching for junctions via segment mapping
[2019-07-18 00:36:23] Retrieving sequences for splices
[2019-07-18 00:38:34] Indexing splices
[2019-07-18 00:39:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-07-18 00:40:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-07-18 00:41:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-07-18 00:42:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-07-18 00:43:34] Joining segment hits
[2019-07-18 00:47:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-07-18 00:48:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-07-18 00:49:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-07-18 00:50:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-07-18 00:50:40] Joining segment hits
[2019-07-18 00:54:35] Reporting output tracks
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[2019-07-18 01:51:04] A summary of the alignment counts can be found in /scratch/7776706.1.linga/tophat2/align_summary.txt
[2019-07-18 01:51:04] Run complete: 03:22:37 elapsed