[2018-10-13 02:28:36] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:28:36] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:28:36] Checking for Bowtie index files (genome)..
[2018-10-13 02:28:36] Checking for reference FASTA file
[2018-10-13 02:28:36] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:28:41] Reading known junctions from GTF file
[2018-10-13 02:28:46] Preparing reads
	 left reads: min. length=100, max. length=100, 148898 kept reads (201 discarded)
	right reads: min. length=100, max. length=100, 148821 kept reads (278 discarded)
[2018-10-13 02:28:53] Building transcriptome data files /scratch/8792919.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:29:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:38:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:38:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:38:54] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:38:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:39:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:39:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:39:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:39:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:40:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:40:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:40:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:40:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:40:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:41:10] Searching for junctions via segment mapping
[2018-10-13 02:43:40] Retrieving sequences for splices
[2018-10-13 02:45:51] Indexing splices
[2018-10-13 02:46:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:46:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:46:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:46:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:46:30] Joining segment hits
[2018-10-13 02:48:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:48:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:48:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:49:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:49:07] Joining segment hits
[2018-10-13 02:51:21] Reporting output tracks
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[2018-10-13 02:54:00] A summary of the alignment counts can be found in /scratch/8792919.1.linga/tophat2/align_summary.txt
[2018-10-13 02:54:00] Run complete: 00:25:24 elapsed