[2018-10-13 03:55:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:55:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:55:58] Checking for Bowtie index files (genome)..
[2018-10-13 03:55:58] Checking for reference FASTA file
[2018-10-13 03:55:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:56:02] Reading known junctions from GTF file
[2018-10-13 03:56:07] Preparing reads
	 left reads: min. length=100, max. length=100, 966345 kept reads (127 discarded)
	right reads: min. length=100, max. length=100, 966106 kept reads (366 discarded)
[2018-10-13 03:56:47] Building transcriptome data files /scratch/8792976.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:57:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:05:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:07:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:08:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:08:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:09:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:09:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:09:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:09:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:10:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:10:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:10:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:11:04] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:11:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:11:29] Searching for junctions via segment mapping
[2018-10-13 04:17:48] Retrieving sequences for splices
[2018-10-13 04:19:53] Indexing splices
[2018-10-13 04:20:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:20:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:20:31] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:20:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:20:47] Joining segment hits
[2018-10-13 04:23:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:23:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:23:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:23:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:23:43] Joining segment hits
[2018-10-13 04:26:57] Reporting output tracks
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[2018-10-13 04:44:17] A summary of the alignment counts can be found in /scratch/8792976.1.linga/tophat2/align_summary.txt
[2018-10-13 04:44:17] Run complete: 00:48:19 elapsed