[2018-10-13 04:03:28] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:03:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:03:28] Checking for Bowtie index files (genome)..
[2018-10-13 04:03:28] Checking for reference FASTA file
[2018-10-13 04:03:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:03:33] Reading known junctions from GTF file
[2018-10-13 04:03:38] Preparing reads
	 left reads: min. length=100, max. length=100, 910805 kept reads (138 discarded)
	right reads: min. length=100, max. length=100, 910573 kept reads (370 discarded)
[2018-10-13 04:04:17] Building transcriptome data files /scratch/8792981.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:04:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:13:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:14:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:15:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:15:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:15:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:16:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:16:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:16:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:16:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:17:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:17:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:17:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:17:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:18:04] Searching for junctions via segment mapping
[2018-10-13 04:23:06] Retrieving sequences for splices
[2018-10-13 04:25:17] Indexing splices
[2018-10-13 04:25:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:25:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:25:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:25:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:26:07] Joining segment hits
[2018-10-13 04:28:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:28:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:28:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:28:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:29:05] Joining segment hits
[2018-10-13 04:31:37] Reporting output tracks
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[2018-10-13 04:45:10] A summary of the alignment counts can be found in /scratch/8792981.1.linga/tophat2/align_summary.txt
[2018-10-13 04:45:10] Run complete: 00:41:41 elapsed