[2018-10-13 12:35:35] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:35:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:35:35] Checking for Bowtie index files (genome)..
[2018-10-13 12:35:35] Checking for reference FASTA file
[2018-10-13 12:35:35] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:35:40] Reading known junctions from GTF file
[2018-10-13 12:35:44] Preparing reads
	 left reads: min. length=100, max. length=100, 557105 kept reads (96 discarded)
	right reads: min. length=100, max. length=100, 556890 kept reads (311 discarded)
[2018-10-13 12:36:09] Building transcriptome data files /scratch/8793235.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:36:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:45:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:45:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:46:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:46:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:47:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:47:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:47:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:47:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:47:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:48:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:48:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:48:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:49:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:49:14] Searching for junctions via segment mapping
[2018-10-13 12:52:30] Retrieving sequences for splices
[2018-10-13 12:55:15] Indexing splices
[2018-10-13 12:55:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:55:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:55:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:55:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:56:03] Joining segment hits
[2018-10-13 12:58:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:58:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:58:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:58:39] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:58:44] Joining segment hits
[2018-10-13 13:01:18] Reporting output tracks
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[2018-10-13 13:06:06] A summary of the alignment counts can be found in /scratch/8793235.1.linga/tophat2/align_summary.txt
[2018-10-13 13:06:06] Run complete: 00:30:30 elapsed