[2018-10-12 23:34:48] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:34:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:34:48] Checking for Bowtie index files (genome)..
[2018-10-12 23:34:48] Checking for reference FASTA file
[2018-10-12 23:34:48] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:34:52] Reading known junctions from GTF file
[2018-10-12 23:34:57] Preparing reads
	 left reads: min. length=100, max. length=100, 296329 kept reads (190 discarded)
	right reads: min. length=100, max. length=100, 296068 kept reads (451 discarded)
[2018-10-12 23:35:11] Building transcriptome data files /scratch/8792841.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:35:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:44:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:45:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:45:46] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:45:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:46:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:46:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:46:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:46:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:47:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:47:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:47:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:48:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:48:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:48:33] Searching for junctions via segment mapping
[2018-10-12 23:51:14] Retrieving sequences for splices
[2018-10-12 23:53:27] Indexing splices
[2018-10-12 23:53:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:53:52] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:53:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:54:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:54:05] Joining segment hits
[2018-10-12 23:56:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:56:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:56:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:56:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:56:50] Joining segment hits
[2018-10-12 23:59:21] Reporting output tracks
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[2018-10-13 00:02:38] A summary of the alignment counts can be found in /scratch/8792841.1.linga/tophat2/align_summary.txt
[2018-10-13 00:02:38] Run complete: 00:27:49 elapsed