[2018-10-13 07:06:20] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:06:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:06:20] Checking for Bowtie index files (genome)..
[2018-10-13 07:06:20] Checking for reference FASTA file
[2018-10-13 07:06:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:06:25] Reading known junctions from GTF file
[2018-10-13 07:06:29] Preparing reads
	 left reads: min. length=100, max. length=100, 1537796 kept reads (130 discarded)
	right reads: min. length=100, max. length=100, 1537242 kept reads (684 discarded)
[2018-10-13 07:07:31] Building transcriptome data files /scratch/8793076.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:07:49] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:15:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:16:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:18:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:18:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:18:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:18:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:19:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:19:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:19:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:20:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:20:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:20:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:20:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:21:12] Searching for junctions via segment mapping
[2018-10-13 07:25:37] Retrieving sequences for splices
[2018-10-13 07:27:49] Indexing splices
Building a SMALL index
[2018-10-13 07:28:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:28:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:28:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:28:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:28:37] Joining segment hits
[2018-10-13 07:31:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:31:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:31:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:31:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:31:45] Joining segment hits
[2018-10-13 07:34:33] Reporting output tracks
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[2018-10-13 07:47:10] A summary of the alignment counts can be found in /scratch/8793076.1.linga/tophat2/align_summary.txt
[2018-10-13 07:47:10] Run complete: 00:40:49 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...