[2018-10-12 23:18:02] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:18:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:18:02] Checking for Bowtie index files (genome)..
[2018-10-12 23:18:02] Checking for reference FASTA file
[2018-10-12 23:18:02] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:18:04] Reading known junctions from GTF file
[2018-10-12 23:18:06] Preparing reads
	 left reads: min. length=100, max. length=100, 3684208 kept reads (524 discarded)
	right reads: min. length=100, max. length=100, 3683431 kept reads (1301 discarded)
[2018-10-12 23:19:36] Building transcriptome data files /scratch/8792835.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:19:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:24:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:28:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:32:52] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:32:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:33:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:34:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:34:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:34:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:35:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:36:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:36:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:36:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:37:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:37:30] Searching for junctions via segment mapping
[2018-10-12 23:53:20] Retrieving sequences for splices
[2018-10-12 23:54:26] Indexing splices
Building a SMALL index
[2018-10-12 23:54:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:54:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:55:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:55:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:55:50] Joining segment hits
[2018-10-12 23:57:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:57:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:57:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:58:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:58:26] Joining segment hits
[2018-10-12 23:59:53] Reporting output tracks
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[2018-10-13 01:13:27] A summary of the alignment counts can be found in /scratch/8792835.1.p16/tophat2/align_summary.txt
[2018-10-13 01:13:27] Run complete: 01:55:25 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...