[2018-10-12 21:44:56] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:44:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:44:56] Checking for Bowtie index files (genome)..
[2018-10-12 21:44:56] Checking for reference FASTA file
[2018-10-12 21:44:56] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:45:00] Reading known junctions from GTF file
[2018-10-12 21:45:05] Preparing reads
	 left reads: min. length=100, max. length=100, 159510 kept reads (97 discarded)
	right reads: min. length=100, max. length=100, 159367 kept reads (240 discarded)
[2018-10-12 21:45:12] Building transcriptome data files /scratch/8792769.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:45:31] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:53:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:54:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:54:34] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:54:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:55:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:55:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:55:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:55:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:55:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:56:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:56:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:56:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:56:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:56:44] Searching for junctions via segment mapping
[2018-10-12 21:59:07] Retrieving sequences for splices
[2018-10-12 22:01:16] Indexing splices
[2018-10-12 22:01:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:01:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:01:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:01:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:01:51] Joining segment hits
[2018-10-12 22:04:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:04:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:04:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:04:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:04:20] Joining segment hits
[2018-10-12 22:06:35] Reporting output tracks
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[2018-10-12 22:09:18] A summary of the alignment counts can be found in /scratch/8792769.1.linga/tophat2/align_summary.txt
[2018-10-12 22:09:18] Run complete: 00:24:21 elapsed