[2018-10-13 13:09:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:09:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:09:05] Checking for Bowtie index files (genome)..
[2018-10-13 13:09:05] Checking for reference FASTA file
[2018-10-13 13:09:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:09:07] Reading known junctions from GTF file
[2018-10-13 13:09:12] Preparing reads
	 left reads: min. length=100, max. length=100, 3337687 kept reads (406 discarded)
	right reads: min. length=100, max. length=100, 3337008 kept reads (1085 discarded)
[2018-10-13 13:10:38] Building transcriptome data files /scratch/8793249.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:10:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:15:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:20:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:24:38] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:24:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:25:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:25:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:26:17] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:26:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:26:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:27:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:28:02] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:28:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:28:47] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:29:07] Searching for junctions via segment mapping
[2018-10-13 13:47:26] Retrieving sequences for splices
[2018-10-13 13:48:31] Indexing splices
Building a SMALL index
[2018-10-13 13:48:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:49:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:49:31] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:49:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:50:18] Joining segment hits
[2018-10-13 13:51:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:51:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:52:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:52:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:53:14] Joining segment hits
[2018-10-13 13:55:26] Reporting output tracks
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[2018-10-13 15:42:26] A summary of the alignment counts can be found in /scratch/8793249.1.linga/tophat2/align_summary.txt
[2018-10-13 15:42:26] Run complete: 02:33:21 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...