[2018-10-13 16:30:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:30:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:30:10] Checking for Bowtie index files (genome)..
[2018-10-13 16:30:10] Checking for reference FASTA file
[2018-10-13 16:30:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:30:15] Reading known junctions from GTF file
[2018-10-13 16:30:21] Preparing reads
	 left reads: min. length=100, max. length=100, 38401 kept reads (54 discarded)
	right reads: min. length=100, max. length=100, 38394 kept reads (61 discarded)
[2018-10-13 16:30:23] Building transcriptome data files /scratch/8793358.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:30:51] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:41:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:41:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:41:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:41:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:41:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:41:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:41:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:41:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:42:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:42:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:42:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:42:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:42:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:42:40] Searching for junctions via segment mapping
[2018-10-13 16:44:55] Retrieving sequences for splices
[2018-10-13 16:47:00] Indexing splices
[2018-10-13 16:47:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:47:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:47:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:47:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:47:34] Joining segment hits
[2018-10-13 16:49:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:49:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:49:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:49:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:50:00] Joining segment hits
[2018-10-13 16:52:06] Reporting output tracks
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[2018-10-13 16:54:26] A summary of the alignment counts can be found in /scratch/8793358.1.linga/tophat2/align_summary.txt
[2018-10-13 16:54:26] Run complete: 00:24:15 elapsed