[2018-10-13 15:28:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:28:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:28:08] Checking for Bowtie index files (genome)..
[2018-10-13 15:28:08] Checking for reference FASTA file
[2018-10-13 15:28:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:28:13] Reading known junctions from GTF file
[2018-10-13 15:28:17] Preparing reads
	 left reads: min. length=100, max. length=100, 271470 kept reads (261 discarded)
	right reads: min. length=100, max. length=100, 271283 kept reads (448 discarded)
[2018-10-13 15:28:28] Building transcriptome data files /scratch/8793320.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:28:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:36:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:37:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:37:51] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:37:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:38:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:38:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:38:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:39:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:39:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:39:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:39:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:40:10] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:40:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:40:30] Searching for junctions via segment mapping
[2018-10-13 15:42:56] Retrieving sequences for splices
[2018-10-13 15:44:57] Indexing splices
[2018-10-13 15:45:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:45:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:45:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:45:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:45:31] Joining segment hits
[2018-10-13 15:47:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:47:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:47:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:47:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:47:55] Joining segment hits
[2018-10-13 15:50:03] Reporting output tracks
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[2018-10-13 15:52:59] A summary of the alignment counts can be found in /scratch/8793320.1.linga/tophat2/align_summary.txt
[2018-10-13 15:52:59] Run complete: 00:24:50 elapsed