[2018-10-13 06:56:33] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:56:33] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:56:33] Checking for Bowtie index files (genome)..
[2018-10-13 06:56:33] Checking for reference FASTA file
[2018-10-13 06:56:33] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:56:37] Reading known junctions from GTF file
[2018-10-13 06:56:41] Preparing reads
	 left reads: min. length=100, max. length=100, 1240360 kept reads (103 discarded)
	right reads: min. length=100, max. length=100, 1240042 kept reads (421 discarded)
[2018-10-13 06:57:29] Building transcriptome data files /scratch/8793072.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:57:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:05:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:06:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:07:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:07:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:07:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:07:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:08:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:08:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:08:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:09:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:09:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:09:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:09:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:09:44] Searching for junctions via segment mapping
[2018-10-13 07:14:02] Retrieving sequences for splices
[2018-10-13 07:16:03] Indexing splices
[2018-10-13 07:16:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:16:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:16:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:16:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:16:48] Joining segment hits
[2018-10-13 07:19:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:19:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:19:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:19:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:19:33] Joining segment hits
[2018-10-13 07:22:03] Reporting output tracks
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[2018-10-13 07:32:00] A summary of the alignment counts can be found in /scratch/8793072.1.linga/tophat2/align_summary.txt
[2018-10-13 07:32:00] Run complete: 00:35:26 elapsed