[2019-04-30 23:27:06] Beginning TopHat run (v2.1.1)
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[2019-04-30 23:27:06] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-30 23:27:06] Checking for Bowtie index files (genome)..
[2019-04-30 23:27:06] Checking for reference FASTA file
[2019-04-30 23:27:06] Generating SAM header for Bowtie2Index/genome
[2019-04-30 23:27:08] Reading known junctions from GTF file
[2019-04-30 23:27:10] Preparing reads
	 left reads: min. length=76, max. length=76, 47550457 kept reads (11595 discarded)
	right reads: min. length=76, max. length=76, 47529570 kept reads (32482 discarded)
[2019-04-30 23:45:54] Building transcriptome data files /scratch/5785979.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-04-30 23:46:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-30 23:50:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:07:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:24:47] Resuming TopHat pipeline with unmapped reads
[2019-05-01 00:24:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:30:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:31:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:31:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:32:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:38:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:39:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:40:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:41:29] Searching for junctions via segment mapping
[2019-05-01 00:51:33] Retrieving sequences for splices
[2019-05-01 00:52:35] Indexing splices
[2019-05-01 00:53:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 00:53:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 00:53:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 00:54:17] Joining segment hits
[2019-05-01 00:55:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 00:56:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 00:56:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 00:57:16] Joining segment hits
[2019-05-01 00:58:48] Reporting output tracks
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[2019-05-01 01:54:15] A summary of the alignment counts can be found in /scratch/5785979.1.p16/tophat2/align_summary.txt
[2019-05-01 01:54:15] Run complete: 02:27:09 elapsed