[2019-04-29 17:44:42] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:44:42] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:44:42] Checking for Bowtie index files (genome)..
[2019-04-29 17:44:42] Checking for reference FASTA file
[2019-04-29 17:44:42] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:44:46] Reading known junctions from GTF file
[2019-04-29 17:44:51] Preparing reads
	 left reads: min. length=50, max. length=50, 47412048 kept reads (6779 discarded)
	right reads: min. length=50, max. length=50, 47409791 kept reads (9036 discarded)
[2019-04-29 18:06:15] Building transcriptome data files /scratch/5765376.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 18:06:34] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 18:15:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:54:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 19:36:56] Resuming TopHat pipeline with unmapped reads
[2019-04-29 19:36:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 19:49:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 19:52:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 19:53:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 20:03:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 20:05:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 20:06:37] Searching for junctions via segment mapping
[2019-04-29 20:12:38] Retrieving sequences for splices
[2019-04-29 20:14:52] Indexing splices
[2019-04-29 20:15:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 20:15:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 20:15:50] Joining segment hits
[2019-04-29 20:18:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 20:18:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 20:19:04] Joining segment hits
[2019-04-29 20:21:44] Reporting output tracks
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[2019-04-29 21:37:42] A summary of the alignment counts can be found in /scratch/5765376.1.linga/tophat2/align_summary.txt
[2019-04-29 21:37:42] Run complete: 03:52:59 elapsed