[2018-10-13 05:05:22] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:05:22] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:05:22] Checking for Bowtie index files (genome)..
[2018-10-13 05:05:22] Checking for reference FASTA file
[2018-10-13 05:05:22] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:05:27] Reading known junctions from GTF file
[2018-10-13 05:05:31] Preparing reads
	 left reads: min. length=100, max. length=100, 1166607 kept reads (211 discarded)
	right reads: min. length=100, max. length=100, 1166329 kept reads (489 discarded)
[2018-10-13 05:06:17] Building transcriptome data files /scratch/8793012.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:06:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:15:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:18:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:21:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:21:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:21:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:22:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:22:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:22:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:23:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:23:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:24:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:24:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:25:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:25:20] Searching for junctions via segment mapping
[2018-10-13 05:39:39] Retrieving sequences for splices
[2018-10-13 05:41:49] Indexing splices
[2018-10-13 05:42:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:42:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:43:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:43:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:43:41] Joining segment hits
[2018-10-13 05:46:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:46:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:47:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:47:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:47:46] Joining segment hits
[2018-10-13 05:50:35] Reporting output tracks
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[2018-10-13 06:33:58] A summary of the alignment counts can be found in /scratch/8793012.1.linga/tophat2/align_summary.txt
[2018-10-13 06:33:58] Run complete: 01:28:36 elapsed