[2018-10-12 23:45:21] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:45:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:45:21] Checking for Bowtie index files (genome)..
[2018-10-12 23:45:21] Checking for reference FASTA file
[2018-10-12 23:45:21] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:45:26] Reading known junctions from GTF file
[2018-10-12 23:45:32] Preparing reads
	 left reads: min. length=100, max. length=100, 283765 kept reads (208 discarded)
	right reads: min. length=100, max. length=100, 283347 kept reads (626 discarded)
[2018-10-12 23:45:47] Building transcriptome data files /scratch/8792847.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:46:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:55:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:55:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:56:23] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:56:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:57:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:57:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:57:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:57:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:57:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:58:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:58:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:58:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:58:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:59:03] Searching for junctions via segment mapping
[2018-10-13 00:01:38] Retrieving sequences for splices
[2018-10-13 00:03:52] Indexing splices
[2018-10-13 00:04:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:04:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:04:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:04:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:04:30] Joining segment hits
[2018-10-13 00:06:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:06:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:06:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:07:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:07:06] Joining segment hits
[2018-10-13 00:09:23] Reporting output tracks
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[2018-10-13 00:12:35] A summary of the alignment counts can be found in /scratch/8792847.1.linga/tophat2/align_summary.txt
[2018-10-13 00:12:35] Run complete: 00:27:14 elapsed