[2018-10-13 02:19:49] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:19:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:19:49] Checking for Bowtie index files (genome)..
[2018-10-13 02:19:49] Checking for reference FASTA file
[2018-10-13 02:19:49] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:19:53] Reading known junctions from GTF file
[2018-10-13 02:19:58] Preparing reads
	 left reads: min. length=100, max. length=100, 409239 kept reads (291 discarded)
	right reads: min. length=100, max. length=100, 408910 kept reads (620 discarded)
[2018-10-13 02:20:16] Building transcriptome data files /scratch/8792911.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:20:35] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:29:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:29:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:30:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:30:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:31:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:31:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:31:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:31:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:31:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:32:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:32:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:32:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:33:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:33:14] Searching for junctions via segment mapping
[2018-10-13 02:36:01] Retrieving sequences for splices
[2018-10-13 02:38:15] Indexing splices
[2018-10-13 02:38:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:38:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:38:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:38:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:38:51] Joining segment hits
[2018-10-13 02:41:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:41:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:41:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:41:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:41:26] Joining segment hits
[2018-10-13 02:44:05] Reporting output tracks
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[2018-10-13 02:48:00] A summary of the alignment counts can be found in /scratch/8792911.1.linga/tophat2/align_summary.txt
[2018-10-13 02:48:00] Run complete: 00:28:11 elapsed