[2018-10-13 04:14:33] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:14:33] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:14:33] Checking for Bowtie index files (genome)..
[2018-10-13 04:14:33] Checking for reference FASTA file
[2018-10-13 04:14:33] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:14:37] Reading known junctions from GTF file
[2018-10-13 04:14:41] Preparing reads
	 left reads: min. length=100, max. length=100, 1125575 kept reads (100 discarded)
	right reads: min. length=100, max. length=100, 1125093 kept reads (582 discarded)
[2018-10-13 04:15:28] Building transcriptome data files /scratch/8792987.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:15:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:23:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:24:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:25:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:25:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:26:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:26:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:26:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:26:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:27:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:27:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:27:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:28:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:28:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:28:38] Searching for junctions via segment mapping
[2018-10-13 04:32:17] Retrieving sequences for splices
[2018-10-13 04:34:28] Indexing splices
[2018-10-13 04:34:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:34:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:35:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:35:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:35:12] Joining segment hits
[2018-10-13 04:37:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:37:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:37:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:38:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:38:06] Joining segment hits
[2018-10-13 04:40:36] Reporting output tracks
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[2018-10-13 04:50:29] A summary of the alignment counts can be found in /scratch/8792987.1.linga/tophat2/align_summary.txt
[2018-10-13 04:50:29] Run complete: 00:35:56 elapsed