[2018-10-13 05:15:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:15:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:15:31] Checking for Bowtie index files (genome)..
[2018-10-13 05:15:31] Checking for reference FASTA file
[2018-10-13 05:15:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:15:35] Reading known junctions from GTF file
[2018-10-13 05:15:39] Preparing reads
	 left reads: min. length=100, max. length=100, 953816 kept reads (130 discarded)
	right reads: min. length=100, max. length=100, 953538 kept reads (408 discarded)
[2018-10-13 05:16:19] Building transcriptome data files /scratch/8793018.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:16:38] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:24:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:26:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:27:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:27:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:28:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:28:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:28:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:29:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:29:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:30:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:30:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:30:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:30:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:31:00] Searching for junctions via segment mapping
[2018-10-13 05:38:51] Retrieving sequences for splices
[2018-10-13 05:41:03] Indexing splices
[2018-10-13 05:41:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:41:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:41:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:42:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:42:15] Joining segment hits
[2018-10-13 05:44:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:44:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:45:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:45:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:45:29] Joining segment hits
[2018-10-13 05:48:03] Reporting output tracks
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[2018-10-13 06:08:57] A summary of the alignment counts can be found in /scratch/8793018.1.linga/tophat2/align_summary.txt
[2018-10-13 06:08:57] Run complete: 00:53:26 elapsed