[2018-10-13 02:43:20] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:43:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:43:20] Checking for Bowtie index files (genome)..
[2018-10-13 02:43:20] Checking for reference FASTA file
[2018-10-13 02:43:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:43:22] Reading known junctions from GTF file
[2018-10-13 02:43:24] Preparing reads
	 left reads: min. length=100, max. length=100, 239362 kept reads (137 discarded)
	right reads: min. length=100, max. length=100, 239172 kept reads (327 discarded)
[2018-10-13 02:43:32] Building transcriptome data files /scratch/8792927.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:43:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:48:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:48:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:49:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:49:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:49:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:49:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:49:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:49:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:49:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:49:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:50:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:50:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:50:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:50:15] Searching for junctions via segment mapping
[2018-10-13 02:51:35] Retrieving sequences for splices
[2018-10-13 02:52:42] Indexing splices
[2018-10-13 02:52:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:52:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:52:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:52:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:53:01] Joining segment hits
[2018-10-13 02:54:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:54:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:54:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:54:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:54:19] Joining segment hits
[2018-10-13 02:55:28] Reporting output tracks
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[2018-10-13 02:57:02] A summary of the alignment counts can be found in /scratch/8792927.1.p8/tophat2/align_summary.txt
[2018-10-13 02:57:02] Run complete: 00:13:41 elapsed