[2018-10-12 22:38:27] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:38:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:38:27] Checking for Bowtie index files (genome)..
[2018-10-12 22:38:27] Checking for reference FASTA file
[2018-10-12 22:38:27] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:38:31] Reading known junctions from GTF file
[2018-10-12 22:38:36] Preparing reads
	 left reads: min. length=100, max. length=100, 445386 kept reads (315 discarded)
	right reads: min. length=100, max. length=100, 445118 kept reads (583 discarded)
[2018-10-12 22:38:56] Building transcriptome data files /scratch/8792806.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:39:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:48:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:49:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:50:03] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:50:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:50:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:51:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:51:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:51:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:51:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:52:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:52:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:52:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:53:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:53:12] Searching for junctions via segment mapping
[2018-10-12 22:56:05] Retrieving sequences for splices
[2018-10-12 22:58:21] Indexing splices
[2018-10-12 22:58:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:58:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:58:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:58:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:59:00] Joining segment hits
[2018-10-12 23:01:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:01:43] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:01:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:01:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:01:57] Joining segment hits
[2018-10-12 23:04:31] Reporting output tracks
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[2018-10-12 23:08:22] A summary of the alignment counts can be found in /scratch/8792806.1.linga/tophat2/align_summary.txt
[2018-10-12 23:08:22] Run complete: 00:29:54 elapsed