[2018-10-13 10:33:48] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:33:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:33:48] Checking for Bowtie index files (genome)..
[2018-10-13 10:33:48] Checking for reference FASTA file
[2018-10-13 10:33:48] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:33:52] Reading known junctions from GTF file
[2018-10-13 10:33:56] Preparing reads
	 left reads: min. length=100, max. length=100, 740638 kept reads (82 discarded)
	right reads: min. length=100, max. length=100, 740441 kept reads (279 discarded)
[2018-10-13 10:34:26] Building transcriptome data files /scratch/8793179.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:34:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:43:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:43:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:44:15] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:44:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:44:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:44:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:45:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:45:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:45:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:45:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:46:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:46:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:46:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:46:32] Searching for junctions via segment mapping
[2018-10-13 10:50:06] Retrieving sequences for splices
[2018-10-13 10:52:09] Indexing splices
[2018-10-13 10:52:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:52:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:52:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:52:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:52:50] Joining segment hits
[2018-10-13 10:55:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:55:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:55:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:55:23] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:55:28] Joining segment hits
[2018-10-13 10:57:52] Reporting output tracks
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[2018-10-13 11:03:26] A summary of the alignment counts can be found in /scratch/8793179.1.linga/tophat2/align_summary.txt
[2018-10-13 11:03:26] Run complete: 00:29:38 elapsed