[2018-10-13 04:45:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:45:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:45:31] Checking for Bowtie index files (genome)..
[2018-10-13 04:45:31] Checking for reference FASTA file
[2018-10-13 04:45:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:45:35] Reading known junctions from GTF file
[2018-10-13 04:45:39] Preparing reads
	 left reads: min. length=100, max. length=100, 614762 kept reads (83 discarded)
	right reads: min. length=100, max. length=100, 614569 kept reads (276 discarded)
[2018-10-13 04:46:06] Building transcriptome data files /scratch/8793001.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:46:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:54:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:55:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:55:54] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:55:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:56:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:56:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:56:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:56:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:56:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:57:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:57:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:57:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:57:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:57:52] Searching for junctions via segment mapping
[2018-10-13 05:01:36] Retrieving sequences for splices
[2018-10-13 05:03:45] Indexing splices
[2018-10-13 05:04:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:04:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:04:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:04:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:04:26] Joining segment hits
[2018-10-13 05:06:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:06:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:07:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:07:08] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:07:13] Joining segment hits
[2018-10-13 05:09:41] Reporting output tracks
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[2018-10-13 05:17:30] A summary of the alignment counts can be found in /scratch/8793001.1.linga/tophat2/align_summary.txt
[2018-10-13 05:17:30] Run complete: 00:31:59 elapsed