[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 02:19:57] Preparing reads
	 left reads: min. length=100, max. length=100, 448247 kept reads (298 discarded)
	right reads: min. length=100, max. length=100, 447796 kept reads (749 discarded)
[2018-10-13 02:20:16] Building transcriptome data files /scratch/8792910.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:20:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:28:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:29:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:29:50] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:29:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:30:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:30:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:30:59] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:31:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:31:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:32:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:32:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:32:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:32:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:32:53] Searching for junctions via segment mapping
[2018-10-13 02:35:36] Retrieving sequences for splices
[2018-10-13 02:37:45] Indexing splices
[2018-10-13 02:38:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:38:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:38:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:38:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:38:24] Joining segment hits
[2018-10-13 02:40:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:40:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:41:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:41:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:41:11] Joining segment hits
[2018-10-13 02:43:38] Reporting output tracks
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[2018-10-13 02:47:28] A summary of the alignment counts can be found in /scratch/8792910.1.linga/tophat2/align_summary.txt
[2018-10-13 02:47:28] Run complete: 00:27:39 elapsed