[2018-10-13 05:23:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:23:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:23:56] Checking for Bowtie index files (genome)..
[2018-10-13 05:23:56] Checking for reference FASTA file
[2018-10-13 05:23:56] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:24:01] Reading known junctions from GTF file
[2018-10-13 05:24:06] Preparing reads
	 left reads: min. length=100, max. length=100, 1106903 kept reads (81 discarded)
	right reads: min. length=100, max. length=100, 1106690 kept reads (294 discarded)
[2018-10-13 05:24:58] Building transcriptome data files /scratch/8793025.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:25:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:33:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:34:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:36:03] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:36:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:36:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:36:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:37:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:37:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:37:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:38:10] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:38:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:38:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:38:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:38:56] Searching for junctions via segment mapping
[2018-10-13 05:43:08] Retrieving sequences for splices
[2018-10-13 05:45:17] Indexing splices
[2018-10-13 05:45:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:45:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:45:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:45:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:46:04] Joining segment hits
[2018-10-13 05:48:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:48:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:48:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:48:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:48:58] Joining segment hits
[2018-10-13 05:51:28] Reporting output tracks
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[2018-10-13 06:01:37] A summary of the alignment counts can be found in /scratch/8793025.1.linga/tophat2/align_summary.txt
[2018-10-13 06:01:37] Run complete: 00:37:41 elapsed