[2018-10-13 05:16:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:16:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:16:44] Checking for Bowtie index files (genome)..
[2018-10-13 05:16:44] Checking for reference FASTA file
[2018-10-13 05:16:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:16:50] Reading known junctions from GTF file
[2018-10-13 05:16:55] Preparing reads
	 left reads: min. length=100, max. length=100, 818821 kept reads (134 discarded)
	right reads: min. length=100, max. length=100, 818597 kept reads (358 discarded)
[2018-10-13 05:17:30] Building transcriptome data files /scratch/8793019.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:17:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:26:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:27:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:28:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:28:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:28:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:29:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:29:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:29:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:29:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:30:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:30:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:30:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:30:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:30:53] Searching for junctions via segment mapping
[2018-10-13 05:35:57] Retrieving sequences for splices
[2018-10-13 05:38:07] Indexing splices
[2018-10-13 05:38:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:38:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:38:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:38:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:39:03] Joining segment hits
[2018-10-13 05:41:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:41:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:41:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:42:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:42:11] Joining segment hits
[2018-10-13 05:45:00] Reporting output tracks
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[2018-10-13 05:59:54] A summary of the alignment counts can be found in /scratch/8793019.1.linga/tophat2/align_summary.txt
[2018-10-13 05:59:54] Run complete: 00:43:10 elapsed