[2018-10-13 03:06:25] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:06:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:06:25] Checking for Bowtie index files (genome)..
[2018-10-13 03:06:25] Checking for reference FASTA file
[2018-10-13 03:06:25] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:06:27] Reading known junctions from GTF file
[2018-10-13 03:06:30] Preparing reads
	 left reads: min. length=100, max. length=100, 54037 kept reads (83 discarded)
	right reads: min. length=100, max. length=100, 54025 kept reads (95 discarded)
[2018-10-13 03:06:31] Building transcriptome data files /scratch/8792942.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:06:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:12:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:12:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:12:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:12:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:12:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:12:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:12:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:13:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:13:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:13:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:13:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:13:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:13:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:13:26] Searching for junctions via segment mapping
[2018-10-13 03:14:39] Retrieving sequences for splices
[2018-10-13 03:15:52] Indexing splices
[2018-10-13 03:16:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:16:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:16:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:16:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:16:11] Joining segment hits
[2018-10-13 03:17:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:17:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:17:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:17:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:17:33] Joining segment hits
[2018-10-13 03:18:47] Reporting output tracks
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[2018-10-13 03:20:02] A summary of the alignment counts can be found in /scratch/8792942.1.c/tophat2/align_summary.txt
[2018-10-13 03:20:02] Run complete: 00:13:37 elapsed