[2018-10-13 11:57:41] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 11:57:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:57:41] Checking for Bowtie index files (genome)..
[2018-10-13 11:57:41] Checking for reference FASTA file
[2018-10-13 11:57:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:57:43] Reading known junctions from GTF file
[2018-10-13 11:57:45] Preparing reads
	 left reads: min. length=100, max. length=100, 1082702 kept reads (251 discarded)
	right reads: min. length=100, max. length=100, 1082489 kept reads (464 discarded)
[2018-10-13 11:58:15] Building transcriptome data files /scratch/8793222.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:58:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:03:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:04:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:04:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:04:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:05:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:05:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:05:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:05:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:05:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:06:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:06:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:06:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:06:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:06:54] Searching for junctions via segment mapping
[2018-10-13 12:11:37] Retrieving sequences for splices
[2018-10-13 12:12:44] Indexing splices
Building a SMALL index
[2018-10-13 12:12:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:13:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:13:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:13:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:13:17] Joining segment hits
[2018-10-13 12:14:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:14:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:14:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:14:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:14:55] Joining segment hits
[2018-10-13 12:16:12] Reporting output tracks
-----------------------------------------------
[2018-10-13 12:26:44] A summary of the alignment counts can be found in /scratch/8793222.1.p8/tophat2/align_summary.txt
[2018-10-13 12:26:44] Run complete: 00:29:03 elapsed
[samopen] SAM header is present: 114 sequences.