[2018-10-13 18:34:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:34:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:34:31] Checking for Bowtie index files (genome)..
[2018-10-13 18:34:31] Checking for reference FASTA file
[2018-10-13 18:34:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:34:35] Reading known junctions from GTF file
[2018-10-13 18:34:40] Preparing reads
	 left reads: min. length=100, max. length=100, 283332 kept reads (205 discarded)
	right reads: min. length=100, max. length=100, 283078 kept reads (459 discarded)
[2018-10-13 18:34:53] Building transcriptome data files /scratch/8793444.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:35:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:44:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:44:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:45:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:45:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:45:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:45:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:45:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:46:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:46:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:46:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:46:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:47:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:47:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:47:20] Searching for junctions via segment mapping
[2018-10-13 18:49:58] Retrieving sequences for splices
[2018-10-13 18:52:12] Indexing splices
[2018-10-13 18:52:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:52:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:52:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:52:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:52:51] Joining segment hits
[2018-10-13 18:55:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:55:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:55:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:55:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:55:25] Joining segment hits
[2018-10-13 18:57:47] Reporting output tracks
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[2018-10-13 19:00:42] A summary of the alignment counts can be found in /scratch/8793444.1.linga/tophat2/align_summary.txt
[2018-10-13 19:00:42] Run complete: 00:26:11 elapsed