[2018-10-13 18:36:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:36:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:36:44] Checking for Bowtie index files (genome)..
[2018-10-13 18:36:44] Checking for reference FASTA file
[2018-10-13 18:36:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:36:48] Reading known junctions from GTF file
[2018-10-13 18:36:52] Preparing reads
	 left reads: min. length=100, max. length=100, 337160 kept reads (229 discarded)
	right reads: min. length=100, max. length=100, 336907 kept reads (482 discarded)
[2018-10-13 18:37:06] Building transcriptome data files /scratch/8793447.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:37:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:44:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:45:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:45:47] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:45:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:46:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:46:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:46:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:46:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:46:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:47:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:47:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:47:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:47:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:48:04] Searching for junctions via segment mapping
[2018-10-13 18:50:42] Retrieving sequences for splices
[2018-10-13 18:52:48] Indexing splices
[2018-10-13 18:53:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:53:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:53:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:53:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:53:26] Joining segment hits
[2018-10-13 18:55:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:55:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:55:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:55:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:55:59] Joining segment hits
[2018-10-13 18:58:56] Reporting output tracks
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[2018-10-13 19:01:56] A summary of the alignment counts can be found in /scratch/8793447.1.linga/tophat2/align_summary.txt
[2018-10-13 19:01:56] Run complete: 00:25:11 elapsed