[2018-10-12 23:31:57] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:31:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:31:58] Checking for Bowtie index files (genome)..
[2018-10-12 23:31:58] Checking for reference FASTA file
[2018-10-12 23:31:58] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:32:02] Reading known junctions from GTF file
[2018-10-12 23:32:06] Preparing reads
	 left reads: min. length=100, max. length=100, 2258955 kept reads (272 discarded)
	right reads: min. length=100, max. length=100, 2258359 kept reads (868 discarded)
[2018-10-12 23:33:34] Building transcriptome data files /scratch/8792838.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:33:53] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:44:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:48:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:50:51] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:50:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:51:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:52:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:52:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:52:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:53:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:54:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:54:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:54:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:55:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:55:30] Searching for junctions via segment mapping
[2018-10-13 00:04:13] Retrieving sequences for splices
[2018-10-13 00:06:16] Indexing splices
Building a SMALL index
[2018-10-13 00:06:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:06:52] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:07:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:07:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:07:38] Joining segment hits
[2018-10-13 00:10:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:10:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:10:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:10:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:11:08] Joining segment hits
[2018-10-13 00:14:23] Reporting output tracks
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[2018-10-13 00:51:01] A summary of the alignment counts can be found in /scratch/8792838.1.linga/tophat2/align_summary.txt
[2018-10-13 00:51:01] Run complete: 01:19:03 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...