[2018-10-13 03:28:27] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:28:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:28:27] Checking for Bowtie index files (genome)..
[2018-10-13 03:28:27] Checking for reference FASTA file
[2018-10-13 03:28:27] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:28:32] Reading known junctions from GTF file
[2018-10-13 03:28:36] Preparing reads
	 left reads: min. length=100, max. length=100, 127301 kept reads (127 discarded)
	right reads: min. length=100, max. length=100, 127197 kept reads (231 discarded)
[2018-10-13 03:28:41] Building transcriptome data files /scratch/8792958.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:29:01] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:36:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:37:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:37:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:37:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:37:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:37:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:38:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:38:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:38:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:38:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:38:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:38:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:39:06] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:39:14] Searching for junctions via segment mapping
[2018-10-13 03:41:37] Retrieving sequences for splices
[2018-10-13 03:43:45] Indexing splices
[2018-10-13 03:44:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:44:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:44:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:44:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:44:21] Joining segment hits
[2018-10-13 03:46:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:46:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:46:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:46:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:46:52] Joining segment hits
[2018-10-13 03:49:07] Reporting output tracks
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[2018-10-13 03:51:37] A summary of the alignment counts can be found in /scratch/8792958.1.linga/tophat2/align_summary.txt
[2018-10-13 03:51:37] Run complete: 00:23:09 elapsed