[2018-10-13 05:20:43] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 05:20:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:20:43] Checking for Bowtie index files (genome)..
[2018-10-13 05:20:43] Checking for reference FASTA file
[2018-10-13 05:20:43] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:20:48] Reading known junctions from GTF file
[2018-10-13 05:20:52] Preparing reads
	 left reads: min. length=100, max. length=100, 488292 kept reads (326 discarded)
	right reads: min. length=100, max. length=100, 487872 kept reads (746 discarded)
[2018-10-13 05:21:13] Building transcriptome data files /scratch/8793022.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:21:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:29:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:30:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:30:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:30:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:31:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:31:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:31:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:31:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:32:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:32:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:32:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:32:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:33:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:33:21] Searching for junctions via segment mapping
[2018-10-13 05:36:52] Retrieving sequences for splices
[2018-10-13 05:38:55] Indexing splices
[2018-10-13 05:39:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:39:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:39:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:39:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:39:34] Joining segment hits
[2018-10-13 05:42:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:42:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:42:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:42:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:42:57] Joining segment hits
[2018-10-13 05:45:13] Reporting output tracks
-----------------------------------------------
[2018-10-13 05:50:38] A summary of the alignment counts can be found in /scratch/8793022.1.linga/tophat2/align_summary.txt
[2018-10-13 05:50:38] Run complete: 00:29:54 elapsed