[2018-10-13 16:44:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:44:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:44:30] Checking for Bowtie index files (genome)..
[2018-10-13 16:44:30] Checking for reference FASTA file
[2018-10-13 16:44:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:44:34] Reading known junctions from GTF file
[2018-10-13 16:44:38] Preparing reads
	 left reads: min. length=100, max. length=100, 583734 kept reads (315 discarded)
	right reads: min. length=100, max. length=100, 583371 kept reads (678 discarded)
[2018-10-13 16:45:04] Building transcriptome data files /scratch/8793370.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:45:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:53:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:53:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:54:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:54:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:55:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:55:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:55:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:56:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:56:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:57:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:57:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:57:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:57:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:58:05] Searching for junctions via segment mapping
[2018-10-13 17:01:06] Retrieving sequences for splices
[2018-10-13 17:03:14] Indexing splices
[2018-10-13 17:03:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:03:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:03:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:03:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:03:56] Joining segment hits
[2018-10-13 17:06:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:06:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:06:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:06:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:06:44] Joining segment hits
[2018-10-13 17:09:13] Reporting output tracks
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[2018-10-13 17:13:15] A summary of the alignment counts can be found in /scratch/8793370.1.linga/tophat2/align_summary.txt
[2018-10-13 17:13:15] Run complete: 00:28:44 elapsed