[2018-10-13 00:23:20] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 00:23:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:23:20] Checking for Bowtie index files (genome)..
[2018-10-13 00:23:20] Checking for reference FASTA file
[2018-10-13 00:23:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:23:25] Reading known junctions from GTF file
[2018-10-13 00:23:31] Preparing reads
	 left reads: min. length=100, max. length=100, 353024 kept reads (233 discarded)
	right reads: min. length=100, max. length=100, 352667 kept reads (590 discarded)
[2018-10-13 00:23:49] Building transcriptome data files /scratch/8792863.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:24:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:33:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:34:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:34:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:34:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:35:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:35:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:36:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:36:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:36:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:37:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:37:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:37:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:37:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:38:01] Searching for junctions via segment mapping
[2018-10-13 00:41:08] Retrieving sequences for splices
[2018-10-13 00:43:37] Indexing splices
[2018-10-13 00:44:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:44:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:44:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:44:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:44:24] Joining segment hits
[2018-10-13 00:47:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:47:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:47:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:47:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:47:30] Joining segment hits
[2018-10-13 00:50:08] Reporting output tracks
-----------------------------------------------
[2018-10-13 00:53:56] A summary of the alignment counts can be found in /scratch/8792863.1.linga/tophat2/align_summary.txt
[2018-10-13 00:53:56] Run complete: 00:30:35 elapsed