[2018-10-13 07:03:38] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:03:38] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:03:38] Checking for Bowtie index files (genome)..
[2018-10-13 07:03:38] Checking for reference FASTA file
[2018-10-13 07:03:38] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:03:40] Reading known junctions from GTF file
[2018-10-13 07:03:42] Preparing reads
	 left reads: min. length=100, max. length=100, 1092543 kept reads (101 discarded)
	right reads: min. length=100, max. length=100, 1092215 kept reads (429 discarded)
[2018-10-13 07:04:14] Building transcriptome data files /scratch/8793075.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:04:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:09:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:09:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:10:33] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:10:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:10:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:10:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:11:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:11:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:11:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:11:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:11:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:11:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:11:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:11:54] Searching for junctions via segment mapping
[2018-10-13 07:14:01] Retrieving sequences for splices
[2018-10-13 07:15:07] Indexing splices
Building a SMALL index
[2018-10-13 07:15:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:15:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:15:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:15:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:15:31] Joining segment hits
[2018-10-13 07:16:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:16:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:16:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:16:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:16:59] Joining segment hits
[2018-10-13 07:18:14] Reporting output tracks
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[2018-10-13 07:24:13] A summary of the alignment counts can be found in /scratch/8793075.1.p8/tophat2/align_summary.txt
[2018-10-13 07:24:13] Run complete: 00:20:34 elapsed
[samopen] SAM header is present: 114 sequences.