[2018-10-12 22:04:12] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:04:12] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:04:12] Checking for Bowtie index files (genome)..
[2018-10-12 22:04:12] Checking for reference FASTA file
[2018-10-12 22:04:12] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:04:16] Reading known junctions from GTF file
[2018-10-12 22:04:21] Preparing reads
	 left reads: min. length=100, max. length=100, 154191 kept reads (235 discarded)
	right reads: min. length=100, max. length=100, 154119 kept reads (307 discarded)
[2018-10-12 22:04:28] Building transcriptome data files /scratch/8792782.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:04:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:13:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:14:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:14:31] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:14:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:15:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:15:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:15:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:15:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:15:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:16:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:16:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:16:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:16:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:16:51] Searching for junctions via segment mapping
[2018-10-12 22:19:19] Retrieving sequences for splices
[2018-10-12 22:21:43] Indexing splices
[2018-10-12 22:22:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:22:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:22:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:22:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:22:21] Joining segment hits
[2018-10-12 22:24:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:24:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:24:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:24:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:25:01] Joining segment hits
[2018-10-12 22:27:19] Reporting output tracks
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[2018-10-12 22:30:02] A summary of the alignment counts can be found in /scratch/8792782.1.linga/tophat2/align_summary.txt
[2018-10-12 22:30:02] Run complete: 00:25:49 elapsed