[2019-06-24 17:46:21] Beginning TopHat run (v2.1.1)
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[2019-06-24 17:46:21] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:46:21] Checking for Bowtie index files (genome)..
[2019-06-24 17:46:21] Checking for reference FASTA file
[2019-06-24 17:46:21] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:46:23] Reading known junctions from GTF file
[2019-06-24 17:46:27] Preparing reads
	 left reads: min. length=101, max. length=101, 32367956 kept reads (2311 discarded)
	right reads: min. length=101, max. length=101, 32352686 kept reads (17581 discarded)
[2019-06-24 18:20:48] Building transcriptome data files /scratch/7056785.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:21:06] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:27:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 18:52:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:19:50] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:19:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:36:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 19:39:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 19:41:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 19:44:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 19:47:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:04:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:07:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:11:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:14:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:17:15] Searching for junctions via segment mapping
[2019-06-24 20:55:17] Retrieving sequences for splices
[2019-06-24 20:57:35] Indexing splices
[2019-06-24 20:58:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:00:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:02:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:03:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:05:26] Joining segment hits
[2019-06-24 21:10:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:12:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:14:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:16:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:18:29] Joining segment hits
[2019-06-24 21:24:27] Reporting output tracks
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[2019-06-24 23:45:37] A summary of the alignment counts can be found in /scratch/7056785.1.linga/tophat2/align_summary.txt
[2019-06-24 23:45:37] Run complete: 05:59:16 elapsed