[2018-10-13 08:31:59] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:31:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:31:59] Checking for Bowtie index files (genome)..
[2018-10-13 08:31:59] Checking for reference FASTA file
[2018-10-13 08:31:59] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:32:03] Reading known junctions from GTF file
[2018-10-13 08:32:07] Preparing reads
	 left reads: min. length=100, max. length=100, 789465 kept reads (474 discarded)
	right reads: min. length=100, max. length=100, 789270 kept reads (669 discarded)
[2018-10-13 08:32:39] Building transcriptome data files /scratch/8793119.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:32:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:41:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:42:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:44:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:44:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:45:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:45:12] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:45:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:45:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:45:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:46:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:46:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:47:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:47:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:47:30] Searching for junctions via segment mapping
[2018-10-13 08:55:34] Retrieving sequences for splices
[2018-10-13 08:57:40] Indexing splices
[2018-10-13 08:58:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:58:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:58:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:58:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:58:41] Joining segment hits
[2018-10-13 09:01:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:01:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:01:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:01:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:01:51] Joining segment hits
[2018-10-13 09:04:16] Reporting output tracks
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[2018-10-13 09:27:35] A summary of the alignment counts can be found in /scratch/8793119.1.linga/tophat2/align_summary.txt
[2018-10-13 09:27:35] Run complete: 00:55:36 elapsed