[2018-10-12 22:35:27] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:35:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:35:27] Checking for Bowtie index files (genome)..
[2018-10-12 22:35:27] Checking for reference FASTA file
[2018-10-12 22:35:27] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:35:31] Reading known junctions from GTF file
[2018-10-12 22:35:35] Preparing reads
	 left reads: min. length=100, max. length=100, 541029 kept reads (362 discarded)
	right reads: min. length=100, max. length=100, 540631 kept reads (760 discarded)
[2018-10-12 22:35:59] Building transcriptome data files /scratch/8792802.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:36:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:44:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:45:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:45:59] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:45:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:46:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:47:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:47:16] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:47:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:47:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:48:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:48:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:49:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:49:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:49:25] Searching for junctions via segment mapping
[2018-10-12 22:52:18] Retrieving sequences for splices
[2018-10-12 22:54:22] Indexing splices
[2018-10-12 22:54:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:54:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:54:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:54:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:55:01] Joining segment hits
[2018-10-12 22:57:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:57:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:57:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:57:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:57:48] Joining segment hits
[2018-10-12 23:00:09] Reporting output tracks
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[2018-10-12 23:03:59] A summary of the alignment counts can be found in /scratch/8792802.1.linga/tophat2/align_summary.txt
[2018-10-12 23:03:59] Run complete: 00:28:32 elapsed