[2018-10-13 01:32:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:32:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:32:44] Checking for Bowtie index files (genome)..
[2018-10-13 01:32:44] Checking for reference FASTA file
[2018-10-13 01:32:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:32:49] Reading known junctions from GTF file
[2018-10-13 01:32:54] Preparing reads
	 left reads: min. length=100, max. length=100, 605912 kept reads (390 discarded)
	right reads: min. length=100, max. length=100, 605531 kept reads (771 discarded)
[2018-10-13 01:33:22] Building transcriptome data files /scratch/8792891.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:33:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:41:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:42:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:43:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:43:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:44:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:44:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:44:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:45:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:45:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:46:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:46:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:46:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:46:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:47:06] Searching for junctions via segment mapping
[2018-10-13 01:50:06] Retrieving sequences for splices
[2018-10-13 01:52:07] Indexing splices
[2018-10-13 01:52:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:52:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:52:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:52:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:52:43] Joining segment hits
[2018-10-13 01:55:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:55:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:55:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:55:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:55:32] Joining segment hits
[2018-10-13 01:58:05] Reporting output tracks
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[2018-10-13 02:02:58] A summary of the alignment counts can be found in /scratch/8792891.1.linga/tophat2/align_summary.txt
[2018-10-13 02:02:58] Run complete: 00:30:14 elapsed