[2018-10-13 09:18:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:18:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:18:57] Checking for Bowtie index files (genome)..
[2018-10-13 09:18:57] Checking for reference FASTA file
[2018-10-13 09:18:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:19:02] Reading known junctions from GTF file
[2018-10-13 09:19:06] Preparing reads
	 left reads: min. length=100, max. length=100, 838167 kept reads (508 discarded)
	right reads: min. length=100, max. length=100, 837940 kept reads (735 discarded)
[2018-10-13 09:19:37] Building transcriptome data files /scratch/8793143.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:19:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:28:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:30:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:32:32] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:32:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:33:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:33:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:33:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:34:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:34:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:35:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:35:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:36:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:36:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:36:36] Searching for junctions via segment mapping
[2018-10-13 09:46:43] Retrieving sequences for splices
[2018-10-13 09:49:01] Indexing splices
[2018-10-13 09:49:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:49:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:49:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:50:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:50:24] Joining segment hits
[2018-10-13 09:52:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:52:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:53:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:53:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:53:44] Joining segment hits
[2018-10-13 09:56:09] Reporting output tracks
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[2018-10-13 10:25:01] A summary of the alignment counts can be found in /scratch/8793143.1.linga/tophat2/align_summary.txt
[2018-10-13 10:25:01] Run complete: 01:06:03 elapsed