[2018-10-13 04:17:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:17:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:17:33] Checking for Bowtie index files (genome)..
[2018-10-13 04:17:33] Checking for reference FASTA file
[2018-10-13 04:17:33] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:17:38] Reading known junctions from GTF file
[2018-10-13 04:17:42] Preparing reads
	 left reads: min. length=100, max. length=100, 705403 kept reads (63 discarded)
	right reads: min. length=100, max. length=100, 705030 kept reads (436 discarded)
[2018-10-13 04:18:10] Building transcriptome data files /scratch/8792988.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:18:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:26:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:26:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:27:32] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:27:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:28:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:29:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:29:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:29:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:30:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:31:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:31:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:31:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:32:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:32:27] Searching for junctions via segment mapping
[2018-10-13 04:35:36] Retrieving sequences for splices
[2018-10-13 04:37:40] Indexing splices
[2018-10-13 04:38:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:38:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:38:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:38:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:38:25] Joining segment hits
[2018-10-13 04:40:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:40:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:40:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:41:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:41:08] Joining segment hits
[2018-10-13 04:44:04] Reporting output tracks
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[2018-10-13 04:47:28] A summary of the alignment counts can be found in /scratch/8792988.1.linga/tophat2/align_summary.txt
[2018-10-13 04:47:28] Run complete: 00:29:56 elapsed