[2019-07-05 11:11:51] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:11:51] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:11:51] Checking for Bowtie index files (genome)..
[2019-07-05 11:11:51] Checking for reference FASTA file
[2019-07-05 11:11:51] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:11:53] Reading known junctions from GTF file
[2019-07-05 11:11:57] Preparing reads
	 left reads: min. length=150, max. length=150, 25280246 kept reads (2034 discarded)
	right reads: min. length=150, max. length=150, 25264802 kept reads (17478 discarded)
[2019-07-05 11:39:52] Building transcriptome data files /scratch/7534483.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:40:09] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:46:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:10:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:35:44] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:35:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:52:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:53:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:55:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:56:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:58:19] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:59:52] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:01:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:22:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:24:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:26:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:28:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:31:10] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:33:20] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:35:36] Searching for junctions via segment mapping
[2019-07-05 15:24:13] Retrieving sequences for splices
[2019-07-05 15:26:24] Indexing splices
[2019-07-05 15:27:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:28:52] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:29:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:31:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:32:11] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:33:14] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:34:11] Joining segment hits
[2019-07-05 15:39:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:41:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:43:06] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:44:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:46:48] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:48:29] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:49:57] Joining segment hits
[2019-07-05 15:56:46] Reporting output tracks
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[2019-07-05 17:30:46] A summary of the alignment counts can be found in /scratch/7534483.1.linga/tophat2/align_summary.txt
[2019-07-05 17:30:46] Run complete: 06:18:55 elapsed