[2018-10-13 18:20:26] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:20:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:20:26] Checking for Bowtie index files (genome)..
[2018-10-13 18:20:26] Checking for reference FASTA file
[2018-10-13 18:20:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:20:30] Reading known junctions from GTF file
[2018-10-13 18:20:35] Preparing reads
	 left reads: min. length=100, max. length=100, 373732 kept reads (189 discarded)
	right reads: min. length=100, max. length=100, 373439 kept reads (482 discarded)
[2018-10-13 18:20:52] Building transcriptome data files /scratch/8793433.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:21:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:29:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:30:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:30:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:30:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:31:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:31:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:31:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:31:39] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:31:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:32:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:32:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:32:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:32:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:33:02] Searching for junctions via segment mapping
[2018-10-13 18:35:43] Retrieving sequences for splices
[2018-10-13 18:37:56] Indexing splices
[2018-10-13 18:38:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:38:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:38:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:38:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:38:32] Joining segment hits
[2018-10-13 18:40:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:40:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:40:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:41:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:41:04] Joining segment hits
[2018-10-13 18:43:18] Reporting output tracks
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[2018-10-13 18:46:28] A summary of the alignment counts can be found in /scratch/8793433.1.linga/tophat2/align_summary.txt
[2018-10-13 18:46:28] Run complete: 00:26:02 elapsed