[2017-06-16 10:19:51] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:19:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:19:52] Checking for Bowtie index files (genome)..
[2017-06-16 10:19:52] Checking for reference FASTA file
[2017-06-16 10:19:52] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:20:00] Reading known junctions from GTF file
[2017-06-16 10:20:05] Preparing reads
	 left reads: min. length=101, max. length=101, 14229320 kept reads (31 discarded)
	right reads: min. length=101, max. length=101, 14190142 kept reads (39209 discarded)
[2017-06-16 10:33:44] Building transcriptome data files /scratch/9351452.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:34:00] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:35:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:44:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:52:56] Resuming TopHat pipeline with unmapped reads
[2017-06-16 10:52:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:01:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:03:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:05:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:07:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:09:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:21:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:23:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:26:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:33:47] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:38:11] Searching for junctions via segment mapping
[2017-06-16 12:07:29] Retrieving sequences for splices
[2017-06-16 12:10:30] Indexing splices
[2017-06-16 12:11:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:12:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:14:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:15:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:16:42] Joining segment hits
[2017-06-16 12:20:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:22:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:24:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:25:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:27:15] Joining segment hits
[2017-06-16 12:31:52] Reporting output tracks
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[2017-06-16 12:52:18] A summary of the alignment counts can be found in /scratch/9351452.1.linga/tophat2/align_summary.txt
[2017-06-16 12:52:18] Run complete: 02:32:27 elapsed