[2019-04-30 22:56:55] Beginning TopHat run (v2.1.1)
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[2019-04-30 22:56:55] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-30 22:56:57] Checking for Bowtie index files (genome)..
[2019-04-30 22:56:57] Checking for reference FASTA file
[2019-04-30 22:56:57] Generating SAM header for Bowtie2Index/genome
[2019-04-30 22:57:02] Reading known junctions from GTF file
[2019-04-30 22:57:06] Preparing reads
	 left reads: min. length=76, max. length=76, 31444263 kept reads (6687 discarded)
	right reads: min. length=76, max. length=76, 31427377 kept reads (23573 discarded)
[2019-04-30 23:15:31] Building transcriptome data files /scratch/5785969.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-30 23:15:50] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-30 23:24:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:00:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:35:59] Resuming TopHat pipeline with unmapped reads
[2019-05-01 00:35:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:42:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:44:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:45:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:46:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:54:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:56:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:57:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:59:18] Searching for junctions via segment mapping
[2019-05-01 01:14:27] Retrieving sequences for splices
[2019-05-01 01:16:25] Indexing splices
[2019-05-01 01:17:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:18:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:19:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:19:53] Joining segment hits
[2019-05-01 01:22:55] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:23:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:25:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:26:07] Joining segment hits
[2019-05-01 01:29:11] Reporting output tracks
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[2019-05-01 02:35:50] A summary of the alignment counts can be found in /scratch/5785969.1.linga/tophat2/align_summary.txt
[2019-05-01 02:35:50] Run complete: 03:38:55 elapsed