[2018-10-12 23:03:28] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:03:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:03:28] Checking for Bowtie index files (genome)..
[2018-10-12 23:03:28] Checking for reference FASTA file
[2018-10-12 23:03:28] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:03:30] Reading known junctions from GTF file
[2018-10-12 23:03:32] Preparing reads
	 left reads: min. length=100, max. length=100, 3211057 kept reads (421 discarded)
	right reads: min. length=100, max. length=100, 3210287 kept reads (1191 discarded)
[2018-10-12 23:04:52] Building transcriptome data files /scratch/8792819.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:05:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:09:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:11:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:13:16] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:13:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:14:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:14:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:14:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:14:39] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:14:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:15:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:15:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:16:10] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:16:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:16:35] Searching for junctions via segment mapping
[2018-10-12 23:21:58] Retrieving sequences for splices
[2018-10-12 23:23:05] Indexing splices
Building a SMALL index
[2018-10-12 23:23:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:23:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:23:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:23:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:23:43] Joining segment hits
[2018-10-12 23:25:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:25:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:25:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:25:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:25:32] Joining segment hits
[2018-10-12 23:26:54] Reporting output tracks
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[2018-10-12 23:50:07] A summary of the alignment counts can be found in /scratch/8792819.1.p8/tophat2/align_summary.txt
[2018-10-12 23:50:07] Run complete: 00:46:39 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...