[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 17:46:19] Reading known junctions from GTF file
[2019-06-24 17:46:23] Preparing reads
	 left reads: min. length=101, max. length=101, 49852643 kept reads (608 discarded)
	right reads: min. length=101, max. length=101, 49809539 kept reads (43712 discarded)
[2019-06-24 18:35:53] Building transcriptome data files /scratch/7056782.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:36:14] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:43:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:32:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 20:22:50] Resuming TopHat pipeline with unmapped reads
[2019-06-24 20:22:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:45:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:49:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:53:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:57:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 21:01:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:26:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 21:29:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 21:33:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 21:37:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 21:41:37] Searching for junctions via segment mapping
[2019-06-24 23:02:04] Retrieving sequences for splices
[2019-06-24 23:04:31] Indexing splices
[2019-06-24 23:05:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 23:08:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 23:10:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 23:13:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 23:15:00] Joining segment hits
[2019-06-24 23:22:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 23:24:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 23:27:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 23:30:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 23:32:51] Joining segment hits
[2019-06-24 23:40:01] Reporting output tracks
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[2019-06-25 03:26:19] A summary of the alignment counts can be found in /scratch/7056782.1.linga/tophat2/align_summary.txt
[2019-06-25 03:26:19] Run complete: 09:40:02 elapsed