[2019-04-30 23:03:24] Beginning TopHat run (v2.1.1)
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[2019-04-30 23:03:24] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-30 23:03:25] Checking for Bowtie index files (genome)..
[2019-04-30 23:03:25] Checking for reference FASTA file
[2019-04-30 23:03:25] Generating SAM header for Bowtie2Index/genome
[2019-04-30 23:03:29] Reading known junctions from GTF file
[2019-04-30 23:03:34] Preparing reads
	 left reads: min. length=76, max. length=76, 32092485 kept reads (7425 discarded)
	right reads: min. length=76, max. length=76, 32079587 kept reads (20323 discarded)
[2019-04-30 23:23:19] Building transcriptome data files /scratch/5785970.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-30 23:23:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-30 23:32:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:17:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 01:05:17] Resuming TopHat pipeline with unmapped reads
[2019-05-01 01:05:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 01:11:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 01:13:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 01:14:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 01:16:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 01:23:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 01:25:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 01:26:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 01:28:48] Searching for junctions via segment mapping
[2019-05-01 01:48:37] Retrieving sequences for splices
[2019-05-01 01:50:47] Indexing splices
[2019-05-01 01:51:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 01:53:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 01:54:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 01:55:42] Joining segment hits
[2019-05-01 01:58:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 02:00:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 02:01:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 02:03:07] Joining segment hits
[2019-05-01 02:06:09] Reporting output tracks
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[2019-05-01 03:37:00] A summary of the alignment counts can be found in /scratch/5785970.1.linga/tophat2/align_summary.txt
[2019-05-01 03:37:00] Run complete: 04:33:36 elapsed