[2018-10-13 07:44:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:44:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:44:04] Checking for Bowtie index files (genome)..
[2018-10-13 07:44:04] Checking for reference FASTA file
[2018-10-13 07:44:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:44:08] Reading known junctions from GTF file
[2018-10-13 07:44:12] Preparing reads
	 left reads: min. length=100, max. length=100, 833229 kept reads (658 discarded)
	right reads: min. length=100, max. length=100, 833020 kept reads (867 discarded)
[2018-10-13 07:44:50] Building transcriptome data files /scratch/8793093.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:45:10] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:54:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:55:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:56:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:56:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:57:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:57:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:57:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:58:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:58:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:59:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:59:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:59:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:00:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:00:21] Searching for junctions via segment mapping
[2018-10-13 08:06:26] Retrieving sequences for splices
[2018-10-13 08:08:38] Indexing splices
[2018-10-13 08:09:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:09:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:09:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:09:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:09:33] Joining segment hits
[2018-10-13 08:12:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:12:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:12:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:12:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:12:38] Joining segment hits
[2018-10-13 08:15:08] Reporting output tracks
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[2018-10-13 08:29:01] A summary of the alignment counts can be found in /scratch/8793093.1.linga/tophat2/align_summary.txt
[2018-10-13 08:29:01] Run complete: 00:44:57 elapsed