[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 17:46:26] Reading known junctions from GTF file
[2019-06-24 17:46:29] Preparing reads
	 left reads: min. length=101, max. length=101, 37228833 kept reads (2519 discarded)
	right reads: min. length=101, max. length=101, 37210602 kept reads (20750 discarded)
[2019-06-24 18:25:35] Building transcriptome data files /scratch/7056784.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:25:51] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:32:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:02:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:33:36] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:33:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:52:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 19:55:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 19:57:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:00:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:02:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:25:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:28:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:32:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:36:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:40:10] Searching for junctions via segment mapping
[2019-06-24 21:20:28] Retrieving sequences for splices
[2019-06-24 21:22:52] Indexing splices
[2019-06-24 21:24:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:25:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:27:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:29:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:30:59] Joining segment hits
[2019-06-24 21:37:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:39:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:41:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:44:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:46:02] Joining segment hits
[2019-06-24 21:53:00] Reporting output tracks
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[2019-06-25 00:18:05] A summary of the alignment counts can be found in /scratch/7056784.1.linga/tophat2/align_summary.txt
[2019-06-25 00:18:05] Run complete: 06:31:43 elapsed