[2018-10-13 09:07:49] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:07:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:07:49] Checking for Bowtie index files (genome)..
[2018-10-13 09:07:49] Checking for reference FASTA file
[2018-10-13 09:07:49] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:07:53] Reading known junctions from GTF file
[2018-10-13 09:07:58] Preparing reads
	 left reads: min. length=100, max. length=100, 1310244 kept reads (103 discarded)
	right reads: min. length=100, max. length=100, 1309878 kept reads (469 discarded)
[2018-10-13 09:08:50] Building transcriptome data files /scratch/8793136.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:09:10] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:18:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:19:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:20:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:20:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:21:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:21:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:21:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:22:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:22:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:23:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:23:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:23:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:23:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:24:12] Searching for junctions via segment mapping
[2018-10-13 09:29:25] Retrieving sequences for splices
[2018-10-13 09:31:34] Indexing splices
[2018-10-13 09:31:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:32:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:32:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:32:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:32:26] Joining segment hits
[2018-10-13 09:34:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:35:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:35:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:35:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:35:24] Joining segment hits
[2018-10-13 09:38:38] Reporting output tracks
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[2018-10-13 09:50:06] A summary of the alignment counts can be found in /scratch/8793136.1.linga/tophat2/align_summary.txt
[2018-10-13 09:50:06] Run complete: 00:42:16 elapsed