[2018-10-12 21:26:44] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:26:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:26:44] Checking for Bowtie index files (genome)..
[2018-10-12 21:26:44] Checking for reference FASTA file
[2018-10-12 21:26:44] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:26:46] Reading known junctions from GTF file
[2018-10-12 21:26:49] Preparing reads
	 left reads: min. length=100, max. length=100, 208750 kept reads (157 discarded)
	right reads: min. length=100, max. length=100, 208585 kept reads (322 discarded)
[2018-10-12 21:26:55] Building transcriptome data files /scratch/8792753.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:27:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:31:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:32:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:32:17] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:32:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:32:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:32:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:32:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:32:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:32:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:33:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:33:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:33:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:33:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:33:26] Searching for junctions via segment mapping
[2018-10-12 21:34:41] Retrieving sequences for splices
[2018-10-12 21:35:45] Indexing splices
[2018-10-12 21:35:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:36:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:36:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:36:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:36:08] Joining segment hits
[2018-10-12 21:37:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:37:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:37:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:37:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:37:31] Joining segment hits
[2018-10-12 21:38:42] Reporting output tracks
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[2018-10-12 21:40:05] A summary of the alignment counts can be found in /scratch/8792753.1.linga/tophat2/align_summary.txt
[2018-10-12 21:40:05] Run complete: 00:13:21 elapsed