[2018-10-13 05:19:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:19:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:19:08] Checking for Bowtie index files (genome)..
[2018-10-13 05:19:08] Checking for reference FASTA file
[2018-10-13 05:19:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:19:13] Reading known junctions from GTF file
[2018-10-13 05:19:17] Preparing reads
	 left reads: min. length=100, max. length=100, 1378099 kept reads (98 discarded)
	right reads: min. length=100, max. length=100, 1377647 kept reads (550 discarded)
[2018-10-13 05:20:17] Building transcriptome data files /scratch/8793020.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:20:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:28:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:30:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:31:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:31:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:31:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:31:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:32:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:32:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:32:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:33:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:33:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:33:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:33:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:33:55] Searching for junctions via segment mapping
[2018-10-13 05:38:05] Retrieving sequences for splices
[2018-10-13 05:40:14] Indexing splices
[2018-10-13 05:40:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:40:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:40:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:40:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:41:01] Joining segment hits
[2018-10-13 05:43:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:43:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:43:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:43:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:44:03] Joining segment hits
[2018-10-13 05:46:44] Reporting output tracks
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[2018-10-13 05:58:38] A summary of the alignment counts can be found in /scratch/8793020.1.linga/tophat2/align_summary.txt
[2018-10-13 05:58:38] Run complete: 00:39:29 elapsed