[2018-10-13 13:38:42] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:38:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:38:42] Checking for Bowtie index files (genome)..
[2018-10-13 13:38:42] Checking for reference FASTA file
[2018-10-13 13:38:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:38:44] Reading known junctions from GTF file
[2018-10-13 13:38:47] Preparing reads
	 left reads: min. length=100, max. length=100, 1009909 kept reads (142 discarded)
	right reads: min. length=100, max. length=100, 1009529 kept reads (522 discarded)
[2018-10-13 13:39:14] Building transcriptome data files /scratch/8793268.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:39:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:44:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:45:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:45:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:45:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:46:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:46:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:46:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:46:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:46:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:47:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:47:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:47:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:47:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:47:39] Searching for junctions via segment mapping
[2018-10-13 13:50:16] Retrieving sequences for splices
[2018-10-13 13:51:29] Indexing splices
[2018-10-13 13:51:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:51:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:51:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:51:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:51:53] Joining segment hits
[2018-10-13 13:53:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:53:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:53:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:53:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:53:27] Joining segment hits
[2018-10-13 13:54:49] Reporting output tracks
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[2018-10-13 14:01:39] A summary of the alignment counts can be found in /scratch/8793268.1.c/tophat2/align_summary.txt
[2018-10-13 14:01:39] Run complete: 00:22:57 elapsed