[2019-06-24 17:46:17] Beginning TopHat run (v2.1.1)
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[2019-06-24 17:46:17] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:46:17] Checking for Bowtie index files (genome)..
[2019-06-24 17:46:17] Checking for reference FASTA file
[2019-06-24 17:46:17] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:46:22] Reading known junctions from GTF file
[2019-06-24 17:46:25] Preparing reads
	 left reads: min. length=101, max. length=101, 34856377 kept reads (1633 discarded)
	right reads: min. length=101, max. length=101, 34839666 kept reads (18344 discarded)
[2019-06-24 18:24:18] Building transcriptome data files /scratch/7056780.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:24:35] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:30:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:03:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:37:50] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:37:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:58:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:00:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:03:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:06:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:08:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:29:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:33:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:36:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:40:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:43:40] Searching for junctions via segment mapping
[2019-06-24 21:41:12] Retrieving sequences for splices
[2019-06-24 21:43:33] Indexing splices
[2019-06-24 21:44:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:46:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:47:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:49:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:50:41] Joining segment hits
[2019-06-24 21:56:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:58:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 22:01:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 22:03:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 22:04:56] Joining segment hits
[2019-06-24 22:11:27] Reporting output tracks
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[2019-06-25 00:47:07] A summary of the alignment counts can be found in /scratch/7056780.1.linga/tophat2/align_summary.txt
[2019-06-25 00:47:07] Run complete: 07:00:49 elapsed