[2019-05-01 01:31:19] Beginning TopHat run (v2.1.1)
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[2019-05-01 01:31:19] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-05-01 01:31:20] Checking for Bowtie index files (genome)..
[2019-05-01 01:31:20] Checking for reference FASTA file
[2019-05-01 01:31:20] Generating SAM header for Bowtie2Index/genome
[2019-05-01 01:31:22] Reading known junctions from GTF file
[2019-05-01 01:31:24] Preparing reads
	 left reads: min. length=76, max. length=76, 38592602 kept reads (9133 discarded)
	right reads: min. length=76, max. length=76, 38577312 kept reads (24423 discarded)
[2019-05-01 01:46:23] Building transcriptome data files /scratch/5785982.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-05-01 01:46:32] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-01 01:51:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 02:08:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 02:24:32] Resuming TopHat pipeline with unmapped reads
[2019-05-01 02:24:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 02:28:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 02:29:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 02:30:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 02:30:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 02:35:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 02:36:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 02:37:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 02:37:55] Searching for junctions via segment mapping
[2019-05-01 02:48:33] Retrieving sequences for splices
[2019-05-01 02:49:34] Indexing splices
[2019-05-01 02:50:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 02:50:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 02:50:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 02:51:16] Joining segment hits
[2019-05-01 02:52:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 02:53:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 02:53:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 02:54:08] Joining segment hits
[2019-05-01 02:55:38] Reporting output tracks
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[2019-05-01 03:43:30] A summary of the alignment counts can be found in /scratch/5785982.1.p/tophat2/align_summary.txt
[2019-05-01 03:43:30] Run complete: 02:12:10 elapsed