[2019-09-04 11:18:09] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:18:09] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:18:09] Checking for Bowtie index files (genome)..
[2019-09-04 11:18:09] Checking for reference FASTA file
[2019-09-04 11:18:09] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:18:13] Reading known junctions from GTF file
[2019-09-04 11:18:16] Preparing reads
	 left reads: min. length=150, max. length=150, 34422156 kept reads (9 discarded)
	right reads: min. length=150, max. length=150, 34420844 kept reads (1321 discarded)
[2019-09-04 11:40:16] Building transcriptome data files /scratch/9142556.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:40:28] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:45:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:01:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:16:15] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:16:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 12:50:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 12:55:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 12:59:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 13:04:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 13:09:46] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:13:51] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:16:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:51:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:56:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:02:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:07:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:12:24] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:16:31] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:19:03] Searching for junctions via segment mapping
[2019-09-04 14:31:31] Retrieving sequences for splices
[2019-09-04 14:32:33] Indexing splices
[2019-09-04 14:33:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:34:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:35:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:36:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:37:39] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:38:39] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:39:23] Joining segment hits
[2019-09-04 14:43:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:44:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:45:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:46:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:47:30] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:48:32] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:49:17] Joining segment hits
[2019-09-04 14:52:52] Reporting output tracks
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[2019-09-04 15:19:33] A summary of the alignment counts can be found in /scratch/9142556.1.linga/tophat2/align_summary.txt
[2019-09-04 15:19:33] Run complete: 04:01:23 elapsed