[2018-10-13 00:44:54] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:44:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:44:54] Checking for Bowtie index files (genome)..
[2018-10-13 00:44:54] Checking for reference FASTA file
[2018-10-13 00:44:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:44:59] Reading known junctions from GTF file
[2018-10-13 00:45:04] Preparing reads
	 left reads: min. length=100, max. length=100, 337553 kept reads (222 discarded)
	right reads: min. length=100, max. length=100, 337252 kept reads (523 discarded)
[2018-10-13 00:45:19] Building transcriptome data files /scratch/8792869.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:45:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:53:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:54:22] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:54:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:54:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:55:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:55:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:55:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:56:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:56:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:56:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:56:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:57:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:57:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:57:30] Searching for junctions via segment mapping
[2018-10-13 01:00:02] Retrieving sequences for splices
[2018-10-13 01:02:13] Indexing splices
[2018-10-13 01:02:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:02:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:02:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:02:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:02:49] Joining segment hits
[2018-10-13 01:05:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:05:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:05:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:05:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:05:26] Joining segment hits
[2018-10-13 01:07:45] Reporting output tracks
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[2018-10-13 01:11:09] A summary of the alignment counts can be found in /scratch/8792869.1.linga/tophat2/align_summary.txt
[2018-10-13 01:11:09] Run complete: 00:26:14 elapsed