[2019-06-24 17:46:17] Beginning TopHat run (v2.1.1)
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[2019-06-24 17:46:17] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:46:17] Checking for Bowtie index files (genome)..
[2019-06-24 17:46:17] Checking for reference FASTA file
[2019-06-24 17:46:17] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:46:19] Reading known junctions from GTF file
[2019-06-24 17:46:23] Preparing reads
	 left reads: min. length=101, max. length=101, 33382878 kept reads (1428 discarded)
	right reads: min. length=101, max. length=101, 33367369 kept reads (16937 discarded)
[2019-06-24 18:22:04] Building transcriptome data files /scratch/7056781.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:22:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:28:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:01:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:37:12] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:37:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:52:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 19:54:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 19:56:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 19:58:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:00:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:17:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:19:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:22:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:24:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:27:13] Searching for junctions via segment mapping
[2019-06-24 21:21:56] Retrieving sequences for splices
[2019-06-24 21:24:23] Indexing splices
[2019-06-24 21:25:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:26:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:28:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:30:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:31:34] Joining segment hits
[2019-06-24 21:37:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:38:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:40:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:42:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:43:36] Joining segment hits
[2019-06-24 21:49:33] Reporting output tracks
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[2019-06-25 00:35:30] A summary of the alignment counts can be found in /scratch/7056781.1.linga/tophat2/align_summary.txt
[2019-06-25 00:35:30] Run complete: 06:49:13 elapsed