[2018-10-12 23:54:43] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:54:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:54:43] Checking for Bowtie index files (genome)..
[2018-10-12 23:54:43] Checking for reference FASTA file
[2018-10-12 23:54:43] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:54:48] Reading known junctions from GTF file
[2018-10-12 23:54:53] Preparing reads
	 left reads: min. length=100, max. length=100, 246786 kept reads (172 discarded)
	right reads: min. length=100, max. length=100, 246594 kept reads (364 discarded)
[2018-10-12 23:55:04] Building transcriptome data files /scratch/8792850.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:55:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:04:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:04:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:05:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:05:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:05:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:05:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:05:59] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:06:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:06:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:06:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:07:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:07:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:07:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:07:33] Searching for junctions via segment mapping
[2018-10-13 00:10:01] Retrieving sequences for splices
[2018-10-13 00:12:11] Indexing splices
[2018-10-13 00:12:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:12:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:12:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:12:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:12:47] Joining segment hits
[2018-10-13 00:15:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:15:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:15:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:15:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:15:56] Joining segment hits
[2018-10-13 00:18:23] Reporting output tracks
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[2018-10-13 00:21:39] A summary of the alignment counts can be found in /scratch/8792850.1.linga/tophat2/align_summary.txt
[2018-10-13 00:21:39] Run complete: 00:26:55 elapsed