[2018-10-13 02:50:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:50:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:50:34] Checking for Bowtie index files (genome)..
[2018-10-13 02:50:34] Checking for reference FASTA file
[2018-10-13 02:50:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:50:38] Reading known junctions from GTF file
[2018-10-13 02:50:42] Preparing reads
	 left reads: min. length=100, max. length=100, 48851 kept reads (64 discarded)
	right reads: min. length=100, max. length=100, 48859 kept reads (56 discarded)
[2018-10-13 02:50:44] Building transcriptome data files /scratch/8792931.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:51:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:59:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:59:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:59:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:59:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:59:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:59:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:00:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:00:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:00:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:00:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:00:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:00:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:00:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:01:03] Searching for junctions via segment mapping
[2018-10-13 03:03:13] Retrieving sequences for splices
[2018-10-13 03:05:24] Indexing splices
[2018-10-13 03:05:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:05:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:05:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:05:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:06:01] Joining segment hits
[2018-10-13 03:08:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:08:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:08:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:08:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:08:25] Joining segment hits
[2018-10-13 03:10:36] Reporting output tracks
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[2018-10-13 03:12:54] A summary of the alignment counts can be found in /scratch/8792931.1.linga/tophat2/align_summary.txt
[2018-10-13 03:12:54] Run complete: 00:22:20 elapsed