[2019-05-01 01:16:01] Beginning TopHat run (v2.1.1)
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[2019-05-01 01:16:01] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-05-01 01:16:02] Checking for Bowtie index files (genome)..
[2019-05-01 01:16:02] Checking for reference FASTA file
[2019-05-01 01:16:02] Generating SAM header for Bowtie2Index/genome
[2019-05-01 01:16:04] Reading known junctions from GTF file
[2019-05-01 01:16:06] Preparing reads
	 left reads: min. length=76, max. length=76, 37486283 kept reads (9922 discarded)
	right reads: min. length=76, max. length=76, 37472080 kept reads (24125 discarded)
[2019-05-01 01:30:44] Building transcriptome data files /scratch/5785981.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-05-01 01:30:54] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-01 01:35:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 01:47:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 02:00:17] Resuming TopHat pipeline with unmapped reads
[2019-05-01 02:00:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 02:04:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 02:05:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 02:05:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 02:06:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 02:11:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 02:12:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 02:12:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 02:13:40] Searching for junctions via segment mapping
[2019-05-01 02:21:01] Retrieving sequences for splices
[2019-05-01 02:22:01] Indexing splices
[2019-05-01 02:22:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 02:22:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 02:23:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 02:23:21] Joining segment hits
[2019-05-01 02:24:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 02:25:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 02:25:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 02:25:53] Joining segment hits
[2019-05-01 02:27:29] Reporting output tracks
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[2019-05-01 02:56:17] A summary of the alignment counts can be found in /scratch/5785981.1.p16/tophat2/align_summary.txt
[2019-05-01 02:56:17] Run complete: 01:40:16 elapsed