[2018-10-13 13:21:36] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:21:36] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:21:37] Checking for Bowtie index files (genome)..
[2018-10-13 13:21:37] Checking for reference FASTA file
[2018-10-13 13:21:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:21:38] Reading known junctions from GTF file
[2018-10-13 13:21:41] Preparing reads
	 left reads: min. length=100, max. length=100, 963315 kept reads (176 discarded)
	right reads: min. length=100, max. length=100, 963083 kept reads (408 discarded)
[2018-10-13 13:22:07] Building transcriptome data files /scratch/8793260.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:22:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:27:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:28:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:29:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:29:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:29:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:30:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:30:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:30:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:30:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:30:55] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:31:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:31:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:31:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:31:29] Searching for junctions via segment mapping
[2018-10-13 13:36:03] Retrieving sequences for splices
[2018-10-13 13:37:16] Indexing splices
[2018-10-13 13:37:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:37:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:37:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:37:46] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:37:50] Joining segment hits
[2018-10-13 13:39:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:39:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:39:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:39:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:39:34] Joining segment hits
[2018-10-13 13:40:57] Reporting output tracks
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[2018-10-13 13:50:24] A summary of the alignment counts can be found in /scratch/8793260.1.c/tophat2/align_summary.txt
[2018-10-13 13:50:24] Run complete: 00:28:47 elapsed