[2018-10-13 08:30:14] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:30:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:30:14] Checking for Bowtie index files (genome)..
[2018-10-13 08:30:14] Checking for reference FASTA file
[2018-10-13 08:30:14] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:30:19] Reading known junctions from GTF file
[2018-10-13 08:30:23] Preparing reads
	 left reads: min. length=100, max. length=100, 269948 kept reads (140 discarded)
	right reads: min. length=100, max. length=100, 269808 kept reads (280 discarded)
[2018-10-13 08:30:35] Building transcriptome data files /scratch/8793116.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:30:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:39:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:39:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:40:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:40:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:40:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:40:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:41:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:41:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:41:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:41:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:41:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:42:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:42:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:42:20] Searching for junctions via segment mapping
[2018-10-13 08:45:06] Retrieving sequences for splices
[2018-10-13 08:47:15] Indexing splices
[2018-10-13 08:47:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:47:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:47:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:47:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:47:52] Joining segment hits
[2018-10-13 08:50:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:50:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:50:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:50:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:50:23] Joining segment hits
[2018-10-13 08:52:39] Reporting output tracks
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[2018-10-13 08:56:28] A summary of the alignment counts can be found in /scratch/8793116.1.linga/tophat2/align_summary.txt
[2018-10-13 08:56:28] Run complete: 00:26:13 elapsed