[2018-10-13 14:56:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:56:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:56:44] Checking for Bowtie index files (genome)..
[2018-10-13 14:56:44] Checking for reference FASTA file
[2018-10-13 14:56:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:56:49] Reading known junctions from GTF file
[2018-10-13 14:56:53] Preparing reads
	 left reads: min. length=100, max. length=100, 662244 kept reads (61 discarded)
	right reads: min. length=100, max. length=100, 662084 kept reads (221 discarded)
[2018-10-13 14:57:20] Building transcriptome data files /scratch/8793304.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:57:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:06:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:06:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:07:22] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:07:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:07:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:07:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:08:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:08:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:08:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:08:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:08:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:09:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:09:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:09:30] Searching for junctions via segment mapping
[2018-10-13 15:12:31] Retrieving sequences for splices
[2018-10-13 15:14:42] Indexing splices
[2018-10-13 15:15:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:15:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:15:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:15:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:15:20] Joining segment hits
[2018-10-13 15:17:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:17:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:17:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:17:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:17:53] Joining segment hits
[2018-10-13 15:20:10] Reporting output tracks
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[2018-10-13 15:25:23] A summary of the alignment counts can be found in /scratch/8793304.1.linga/tophat2/align_summary.txt
[2018-10-13 15:25:23] Run complete: 00:28:38 elapsed