[2018-10-13 03:55:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:55:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:55:57] Checking for Bowtie index files (genome)..
[2018-10-13 03:55:57] Checking for reference FASTA file
[2018-10-13 03:55:57] 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, 1061794 kept reads (44 discarded)
	right reads: min. length=100, max. length=100, 1061496 kept reads (342 discarded)
[2018-10-13 03:56:55] Building transcriptome data files /scratch/8792974.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:57:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:05:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:06:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:07:17] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:07:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:07:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:07:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:08:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:08:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:08:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:08:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:09:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:09:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:09:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:09:42] Searching for junctions via segment mapping
[2018-10-13 04:13:45] Retrieving sequences for splices
[2018-10-13 04:15:56] Indexing splices
[2018-10-13 04:16:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:16:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:16:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:16:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:16:38] Joining segment hits
[2018-10-13 04:19:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:19:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:19:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:19:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:19:31] Joining segment hits
[2018-10-13 04:22:04] Reporting output tracks
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[2018-10-13 04:30:17] A summary of the alignment counts can be found in /scratch/8792974.1.linga/tophat2/align_summary.txt
[2018-10-13 04:30:17] Run complete: 00:34:20 elapsed