[2018-10-13 00:01:38] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:01:38] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:01:38] Checking for Bowtie index files (genome)..
[2018-10-13 00:01:38] Checking for reference FASTA file
[2018-10-13 00:01:38] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:01:44] Reading known junctions from GTF file
[2018-10-13 00:01:49] Preparing reads
	 left reads: min. length=100, max. length=100, 3341294 kept reads (800 discarded)
	right reads: min. length=100, max. length=100, 3340418 kept reads (1676 discarded)
[2018-10-13 00:04:01] Building transcriptome data files /scratch/8792854.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:04:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:12:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:21:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:30:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:30:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:32:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:33:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:34:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:35:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:36:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:39:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:39:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:41:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:42:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:43:11] Searching for junctions via segment mapping
[2018-10-13 01:13:55] Retrieving sequences for splices
[2018-10-13 01:16:25] Indexing splices
Building a SMALL index
[2018-10-13 01:16:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:17:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:18:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:19:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:20:51] Joining segment hits
[2018-10-13 01:23:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:24:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:25:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:26:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:28:02] Joining segment hits
[2018-10-13 01:31:06] Reporting output tracks
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[2018-10-13 03:52:33] A summary of the alignment counts can be found in /scratch/8792854.1.linga/tophat2/align_summary.txt
[2018-10-13 03:52:33] Run complete: 03:50:55 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...