[2018-10-13 04:30:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:30:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:30:56] Checking for Bowtie index files (genome)..
[2018-10-13 04:30:56] Checking for reference FASTA file
[2018-10-13 04:30:56] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:31:00] Reading known junctions from GTF file
[2018-10-13 04:31:05] Preparing reads
	 left reads: min. length=100, max. length=100, 787407 kept reads (79 discarded)
	right reads: min. length=100, max. length=100, 787198 kept reads (288 discarded)
[2018-10-13 04:31:38] Building transcriptome data files /scratch/8792995.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:31:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:39:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:40:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:41:31] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:41:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:41:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:42:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:42:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:42:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:42:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:43:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:43:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:43:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:43:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:43:44] Searching for junctions via segment mapping
[2018-10-13 04:47:45] Retrieving sequences for splices
[2018-10-13 04:49:57] Indexing splices
[2018-10-13 04:50:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:50:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:50:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:50:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:50:37] Joining segment hits
[2018-10-13 04:53:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:53:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:53:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:53:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:53:24] Joining segment hits
[2018-10-13 04:55:55] Reporting output tracks
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[2018-10-13 05:05:17] A summary of the alignment counts can be found in /scratch/8792995.1.linga/tophat2/align_summary.txt
[2018-10-13 05:05:17] Run complete: 00:34:21 elapsed