[2018-10-13 04:49:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:49:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:49:03] Checking for Bowtie index files (genome)..
[2018-10-13 04:49:03] Checking for reference FASTA file
[2018-10-13 04:49:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:49:08] Reading known junctions from GTF file
[2018-10-13 04:49:12] Preparing reads
	 left reads: min. length=100, max. length=100, 1207431 kept reads (300 discarded)
	right reads: min. length=100, max. length=100, 1207097 kept reads (634 discarded)
[2018-10-13 04:50:00] Building transcriptome data files /scratch/8793009.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:50:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:58:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:01:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:03:40] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:03:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:04:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:04:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:05:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:05:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:05:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:06:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:06:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:07:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:07:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:08:11] Searching for junctions via segment mapping
[2018-10-13 05:21:00] Retrieving sequences for splices
[2018-10-13 05:23:04] Indexing splices
[2018-10-13 05:23:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:23:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:24:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:24:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:24:43] Joining segment hits
[2018-10-13 05:27:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:27:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:27:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:28:14] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:28:30] Joining segment hits
[2018-10-13 05:31:06] Reporting output tracks
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[2018-10-13 06:08:08] A summary of the alignment counts can be found in /scratch/8793009.1.linga/tophat2/align_summary.txt
[2018-10-13 06:08:08] Run complete: 01:19:04 elapsed