[2018-10-12 23:31:52] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:31:52] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:31:52] Checking for Bowtie index files (genome)..
[2018-10-12 23:31:52] Checking for reference FASTA file
[2018-10-12 23:31:52] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:31:54] Reading known junctions from GTF file
[2018-10-12 23:31:56] Preparing reads
	 left reads: min. length=100, max. length=100, 3047035 kept reads (322 discarded)
	right reads: min. length=100, max. length=100, 3044616 kept reads (2741 discarded)
[2018-10-12 23:33:40] Building transcriptome data files /scratch/8792840.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:33:51] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:39:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:40:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:42:54] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:42:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:43:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:43:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:44:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:44:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:44:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:46:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:46:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:46:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:47:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:47:25] Searching for junctions via segment mapping
[2018-10-12 23:55:40] Retrieving sequences for splices
[2018-10-12 23:56:53] Indexing splices
Building a SMALL index
[2018-10-12 23:57:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:57:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:57:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:57:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:57:38] Joining segment hits
[2018-10-12 23:59:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:59:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:59:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:59:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:59:54] Joining segment hits
[2018-10-13 00:01:27] Reporting output tracks
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[2018-10-13 00:22:38] A summary of the alignment counts can be found in /scratch/8792840.1.c/tophat2/align_summary.txt
[2018-10-13 00:22:38] Run complete: 00:50:46 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...