[2019-04-30 22:51:28] Beginning TopHat run (v2.1.1)
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[2019-04-30 22:51:28] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-30 22:51:30] Checking for Bowtie index files (genome)..
[2019-04-30 22:51:30] Checking for reference FASTA file
[2019-04-30 22:51:30] Generating SAM header for Bowtie2Index/genome
[2019-04-30 22:51:58] Reading known junctions from GTF file
[2019-04-30 22:52:03] Preparing reads
	 left reads: min. length=76, max. length=76, 33338292 kept reads (9470 discarded)
	right reads: min. length=76, max. length=76, 33325460 kept reads (22302 discarded)
[2019-04-30 23:13:40] Building transcriptome data files /scratch/5785967.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-30 23:14:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-30 23:22:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:06:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:47:29] Resuming TopHat pipeline with unmapped reads
[2019-05-01 00:47:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:54:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:55:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:56:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:58:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 01:04:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 01:06:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 01:08:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 01:10:17] Searching for junctions via segment mapping
[2019-05-01 01:28:04] Retrieving sequences for splices
[2019-05-01 01:29:56] Indexing splices
[2019-05-01 01:30:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:31:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:32:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:33:43] Joining segment hits
[2019-05-01 01:36:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:38:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:39:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:40:31] Joining segment hits
[2019-05-01 01:43:49] Reporting output tracks
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[2019-05-01 03:00:16] A summary of the alignment counts can be found in /scratch/5785967.1.linga/tophat2/align_summary.txt
[2019-05-01 03:00:16] Run complete: 04:08:47 elapsed