[2018-10-13 06:37:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:37:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:37:40] Checking for Bowtie index files (genome)..
[2018-10-13 06:37:40] Checking for reference FASTA file
[2018-10-13 06:37:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:37:44] Reading known junctions from GTF file
[2018-10-13 06:37:48] Preparing reads
	 left reads: min. length=100, max. length=100, 1485205 kept reads (124 discarded)
	right reads: min. length=100, max. length=100, 1484822 kept reads (507 discarded)
[2018-10-13 06:38:52] Building transcriptome data files /scratch/8793061.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:39:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:46:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:48:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:49:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:49:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:50:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:50:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:50:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:50:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:50:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:51:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:51:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:52:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:52:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:52:28] Searching for junctions via segment mapping
[2018-10-13 06:57:38] Retrieving sequences for splices
[2018-10-13 06:59:44] Indexing splices
[2018-10-13 07:00:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:00:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:00:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:00:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:00:37] Joining segment hits
[2018-10-13 07:03:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:03:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:03:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:03:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:03:31] Joining segment hits
[2018-10-13 07:05:57] Reporting output tracks
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[2018-10-13 07:22:44] A summary of the alignment counts can be found in /scratch/8793061.1.linga/tophat2/align_summary.txt
[2018-10-13 07:22:44] Run complete: 00:45:03 elapsed