[2019-04-30 22:52:22] Beginning TopHat run (v2.1.1)
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[2019-04-30 22:52:22] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-30 22:52:23] Checking for Bowtie index files (genome)..
[2019-04-30 22:52:23] Checking for reference FASTA file
[2019-04-30 22:52:23] Generating SAM header for Bowtie2Index/genome
[2019-04-30 22:52:29] Reading known junctions from GTF file
[2019-04-30 22:52:33] Preparing reads
	 left reads: min. length=76, max. length=76, 31167149 kept reads (6481 discarded)
	right reads: min. length=76, max. length=76, 31153003 kept reads (20627 discarded)
[2019-04-30 23:12:13] Building transcriptome data files /scratch/5785968.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-30 23:12:33] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-30 23:20:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:06:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:52:17] Resuming TopHat pipeline with unmapped reads
[2019-05-01 00:52:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:59:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 01:00:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 01:01:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 01:03:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 01:09:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 01:11:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 01:13:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 01:15:26] Searching for junctions via segment mapping
[2019-05-01 01:34:09] Retrieving sequences for splices
[2019-05-01 01:36:07] Indexing splices
[2019-05-01 01:36:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:38:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:39:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:39:56] Joining segment hits
[2019-05-01 01:42:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:44:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:45:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:46:23] Joining segment hits
[2019-05-01 01:49:27] Reporting output tracks
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[2019-05-01 04:57:16] A summary of the alignment counts can be found in /scratch/5785968.1.linga/tophat2/align_summary.txt
[2019-05-01 04:57:16] Run complete: 06:04:53 elapsed