[2018-10-13 07:57:04] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 07:57:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:57:04] Checking for Bowtie index files (genome)..
[2018-10-13 07:57:04] Checking for reference FASTA file
[2018-10-13 07:57:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:57:08] Reading known junctions from GTF file
[2018-10-13 07:57:13] Preparing reads
	 left reads: min. length=100, max. length=100, 361631 kept reads (242 discarded)
	right reads: min. length=100, max. length=100, 361279 kept reads (594 discarded)
[2018-10-13 07:57:28] Building transcriptome data files /scratch/8793099.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:57:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:06:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:06:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:07:18] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:07:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:07:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:07:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:07:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:08:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:08:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:08:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:08:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:09:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:09:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:09:17] Searching for junctions via segment mapping
[2018-10-13 08:12:00] Retrieving sequences for splices
[2018-10-13 08:14:10] Indexing splices
[2018-10-13 08:14:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:14:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:14:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:14:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:14:48] Joining segment hits
[2018-10-13 08:17:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:17:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:17:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:17:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:17:24] Joining segment hits
[2018-10-13 08:19:49] Reporting output tracks
-----------------------------------------------
[2018-10-13 08:23:39] A summary of the alignment counts can be found in /scratch/8793099.1.linga/tophat2/align_summary.txt
[2018-10-13 08:23:39] Run complete: 00:26:34 elapsed