[2018-10-13 05:23:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:23:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:23:05] Checking for Bowtie index files (genome)..
[2018-10-13 05:23:05] Checking for reference FASTA file
[2018-10-13 05:23:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:23:09] Reading known junctions from GTF file
[2018-10-13 05:23:14] Preparing reads
	 left reads: min. length=100, max. length=100, 1313205 kept reads (100 discarded)
	right reads: min. length=100, max. length=100, 1312650 kept reads (655 discarded)
[2018-10-13 05:24:08] Building transcriptome data files /scratch/8793024.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:24:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:33:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:34:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:35:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:35:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:36:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:36:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:36:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:37:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:37:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:37:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:38:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:38:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:38:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:38:47] Searching for junctions via segment mapping
[2018-10-13 05:43:09] Retrieving sequences for splices
[2018-10-13 05:45:23] Indexing splices
[2018-10-13 05:45:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:45:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:46:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:46:08] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:46:14] Joining segment hits
[2018-10-13 05:48:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:48:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:48:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:49:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:49:09] Joining segment hits
[2018-10-13 05:51:48] Reporting output tracks
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[2018-10-13 06:03:44] A summary of the alignment counts can be found in /scratch/8793024.1.linga/tophat2/align_summary.txt
[2018-10-13 06:03:44] Run complete: 00:40:39 elapsed