[2018-10-13 13:35:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:35:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:35:40] Checking for Bowtie index files (genome)..
[2018-10-13 13:35:40] Checking for reference FASTA file
[2018-10-13 13:35:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:35:44] Reading known junctions from GTF file
[2018-10-13 13:35:49] Preparing reads
	 left reads: min. length=100, max. length=100, 1401520 kept reads (512 discarded)
	right reads: min. length=100, max. length=100, 1401180 kept reads (852 discarded)
[2018-10-13 13:36:44] Building transcriptome data files /scratch/8793265.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:37:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:44:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:46:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:47:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:47:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:48:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:48:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:48:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:49:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:49:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:50:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:50:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:50:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:51:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:51:16] Searching for junctions via segment mapping
[2018-10-13 13:57:20] Retrieving sequences for splices
[2018-10-13 13:59:27] Indexing splices
[2018-10-13 13:59:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:59:59] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:00:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:00:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:00:24] Joining segment hits
[2018-10-13 14:03:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:03:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:03:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:03:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:03:37] Joining segment hits
[2018-10-13 14:06:01] Reporting output tracks
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[2018-10-13 14:22:56] A summary of the alignment counts can be found in /scratch/8793265.1.linga/tophat2/align_summary.txt
[2018-10-13 14:22:56] Run complete: 00:47:16 elapsed