[2018-10-13 07:51:55] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:51:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:51:55] Checking for Bowtie index files (genome)..
[2018-10-13 07:51:55] Checking for reference FASTA file
[2018-10-13 07:51:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:52:00] Reading known junctions from GTF file
[2018-10-13 07:52:04] Preparing reads
	 left reads: min. length=100, max. length=100, 1796492 kept reads (129 discarded)
	right reads: min. length=100, max. length=100, 1795571 kept reads (1050 discarded)
[2018-10-13 07:53:16] Building transcriptome data files /scratch/8793097.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:53:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:01:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:03:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:04:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:04:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:05:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:05:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:05:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:05:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:06:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:06:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:07:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:07:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:07:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:07:52] Searching for junctions via segment mapping
[2018-10-13 08:12:47] Retrieving sequences for splices
[2018-10-13 08:14:49] Indexing splices
[2018-10-13 08:15:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:15:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:15:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:15:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:15:41] Joining segment hits
[2018-10-13 08:18:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:18:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:18:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:18:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:18:42] Joining segment hits
[2018-10-13 08:21:12] Reporting output tracks
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[2018-10-13 08:36:58] A summary of the alignment counts can be found in /scratch/8793097.1.linga/tophat2/align_summary.txt
[2018-10-13 08:36:58] Run complete: 00:45:02 elapsed