[2018-10-13 08:22:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:22:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:22:30] Checking for Bowtie index files (genome)..
[2018-10-13 08:22:30] Checking for reference FASTA file
[2018-10-13 08:22:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:22:34] Reading known junctions from GTF file
[2018-10-13 08:22:38] Preparing reads
	 left reads: min. length=100, max. length=100, 1607793 kept reads (251 discarded)
	right reads: min. length=100, max. length=100, 1607397 kept reads (647 discarded)
[2018-10-13 08:23:40] Building transcriptome data files /scratch/8793112.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:23:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:32:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:33:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:34:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:34:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:35:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:35:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:36:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:36:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:36:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:37:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:37:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:38:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:38:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:38:33] Searching for junctions via segment mapping
[2018-10-13 08:43:13] Retrieving sequences for splices
[2018-10-13 08:45:17] Indexing splices
Building a SMALL index
[2018-10-13 08:45:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:45:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:45:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:45:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:46:03] Joining segment hits
[2018-10-13 08:49:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:49:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:49:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:49:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:49:40] Joining segment hits
[2018-10-13 08:52:20] Reporting output tracks
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[2018-10-13 09:03:09] A summary of the alignment counts can be found in /scratch/8793112.1.linga/tophat2/align_summary.txt
[2018-10-13 09:03:09] Run complete: 00:40:39 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...