[2018-10-12 23:06:47] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:06:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:06:47] Checking for Bowtie index files (genome)..
[2018-10-12 23:06:47] Checking for reference FASTA file
[2018-10-12 23:06:47] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:06:51] Reading known junctions from GTF file
[2018-10-12 23:06:56] Preparing reads
	 left reads: min. length=100, max. length=100, 3315196 kept reads (278 discarded)
	right reads: min. length=100, max. length=100, 3314186 kept reads (1288 discarded)
[2018-10-12 23:09:10] Building transcriptome data files /scratch/8792822.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:09:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:18:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:20:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:22:05] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:22:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:23:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:23:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:24:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:24:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:24:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:26:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:26:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:27:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:27:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:27:46] Searching for junctions via segment mapping
[2018-10-12 23:33:41] Retrieving sequences for splices
[2018-10-12 23:36:06] Indexing splices
[2018-10-12 23:36:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:36:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:36:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:36:55] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:37:04] Joining segment hits
[2018-10-12 23:39:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:40:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:40:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:40:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:40:33] Joining segment hits
[2018-10-12 23:43:27] Reporting output tracks
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[2018-10-13 00:02:32] A summary of the alignment counts can be found in /scratch/8792822.1.linga/tophat2/align_summary.txt
[2018-10-13 00:02:32] Run complete: 00:55:45 elapsed