[2019-07-05 10:55:56] Beginning TopHat run (v2.1.1)
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[2019-07-05 10:55:56] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 10:55:56] Checking for Bowtie index files (genome)..
[2019-07-05 10:55:56] Checking for reference FASTA file
[2019-07-05 10:55:56] Generating SAM header for Bowtie2Index/genome
[2019-07-05 10:55:59] Reading known junctions from GTF file
[2019-07-05 10:56:02] Preparing reads
	 left reads: min. length=150, max. length=150, 23444441 kept reads (1808 discarded)
	right reads: min. length=150, max. length=150, 23430154 kept reads (16095 discarded)
[2019-07-05 11:17:54] Building transcriptome data files /scratch/7534474.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:18:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:21:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:32:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:45:22] Resuming TopHat pipeline with unmapped reads
[2019-07-05 11:45:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 11:54:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 11:55:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 11:55:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 11:56:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 11:57:30] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 11:58:18] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 11:59:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:09:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:10:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:12:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:13:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:14:41] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:15:56] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:17:08] Searching for junctions via segment mapping
[2019-07-05 13:00:04] Retrieving sequences for splices
[2019-07-05 13:01:09] Indexing splices
[2019-07-05 13:01:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:02:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:02:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:03:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:04:00] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:04:31] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:05:00] Joining segment hits
[2019-07-05 13:07:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:08:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:09:04] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:09:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:10:44] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:11:30] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:12:11] Joining segment hits
[2019-07-05 13:15:04] Reporting output tracks
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[2019-07-05 13:47:31] A summary of the alignment counts can be found in /scratch/7534474.1.linga/tophat2/align_summary.txt
[2019-07-05 13:47:31] Run complete: 02:51:34 elapsed