[2018-10-12 23:15:16] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:15:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:15:16] Checking for Bowtie index files (genome)..
[2018-10-12 23:15:16] Checking for reference FASTA file
[2018-10-12 23:15:16] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:15:20] Reading known junctions from GTF file
[2018-10-12 23:15:25] Preparing reads
	 left reads: min. length=100, max. length=100, 302437 kept reads (225 discarded)
	right reads: min. length=100, max. length=100, 302162 kept reads (500 discarded)
[2018-10-12 23:15:38] Building transcriptome data files /scratch/8792831.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:15:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:25:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:25:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:26:07] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:26:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:26:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:26:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:27:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:27:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:27:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:28:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:28:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:28:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:28:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:28:43] Searching for junctions via segment mapping
[2018-10-12 23:31:23] Retrieving sequences for splices
[2018-10-12 23:33:33] Indexing splices
[2018-10-12 23:33:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:34:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:34:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:34:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:34:13] Joining segment hits
[2018-10-12 23:36:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:36:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:36:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:36:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:37:02] Joining segment hits
[2018-10-12 23:39:29] Reporting output tracks
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[2018-10-12 23:43:54] A summary of the alignment counts can be found in /scratch/8792831.1.linga/tophat2/align_summary.txt
[2018-10-12 23:43:54] Run complete: 00:28:37 elapsed