[2018-10-13 09:58:21] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:58:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:58:21] Checking for Bowtie index files (genome)..
[2018-10-13 09:58:21] Checking for reference FASTA file
[2018-10-13 09:58:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:58:25] Reading known junctions from GTF file
[2018-10-13 09:58:30] Preparing reads
	 left reads: min. length=100, max. length=100, 1131343 kept reads (109 discarded)
	right reads: min. length=100, max. length=100, 1131050 kept reads (402 discarded)
[2018-10-13 09:59:14] Building transcriptome data files /scratch/8793160.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:59:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:07:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:09:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:10:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:10:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:11:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:11:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:12:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:12:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:12:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:13:10] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:13:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:13:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:13:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:14:05] Searching for junctions via segment mapping
[2018-10-13 10:20:58] Retrieving sequences for splices
[2018-10-13 10:23:28] Indexing splices
[2018-10-13 10:23:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:24:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:24:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:24:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:24:31] Joining segment hits
[2018-10-13 10:27:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:27:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:27:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:27:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:27:39] Joining segment hits
[2018-10-13 10:30:38] Reporting output tracks
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[2018-10-13 10:51:26] A summary of the alignment counts can be found in /scratch/8793160.1.linga/tophat2/align_summary.txt
[2018-10-13 10:51:26] Run complete: 00:53:04 elapsed