[2018-10-13 03:55:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:55:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:55:58] Checking for Bowtie index files (genome)..
[2018-10-13 03:55:58] Checking for reference FASTA file
[2018-10-13 03:55:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:56:02] Reading known junctions from GTF file
[2018-10-13 03:56:06] Preparing reads
	 left reads: min. length=100, max. length=100, 945578 kept reads (59 discarded)
	right reads: min. length=100, max. length=100, 945373 kept reads (264 discarded)
[2018-10-13 03:56:48] Building transcriptome data files /scratch/8792975.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:57:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:05:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:06:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:08:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:08:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:08:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:08:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:09:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:09:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:09:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:10:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:10:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:10:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:10:57] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:11:09] Searching for junctions via segment mapping
[2018-10-13 04:17:25] Retrieving sequences for splices
[2018-10-13 04:19:26] Indexing splices
[2018-10-13 04:19:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:19:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:20:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:20:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:20:20] Joining segment hits
[2018-10-13 04:23:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:23:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:23:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:23:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:23:44] Joining segment hits
[2018-10-13 04:26:07] Reporting output tracks
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[2018-10-13 04:40:11] A summary of the alignment counts can be found in /scratch/8792975.1.linga/tophat2/align_summary.txt
[2018-10-13 04:40:11] Run complete: 00:44:13 elapsed