[2019-09-04 11:22:24] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:22:24] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:22:24] Checking for Bowtie index files (genome)..
[2019-09-04 11:22:24] Checking for reference FASTA file
[2019-09-04 11:22:24] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:22:28] Reading known junctions from GTF file
[2019-09-04 11:22:32] Preparing reads
	 left reads: min. length=150, max. length=150, 40016649 kept reads (15 discarded)
	right reads: min. length=150, max. length=150, 40015124 kept reads (1540 discarded)
[2019-09-04 12:01:05] Building transcriptome data files /scratch/9142553.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 12:01:24] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 12:11:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:52:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:30:55] Resuming TopHat pipeline with unmapped reads
[2019-09-04 13:30:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:59:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:11:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:23:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:35:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:46:30] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:55:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:59:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 17:33:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 17:43:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 17:54:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 18:07:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 18:18:58] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 18:28:57] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 18:34:15] Searching for junctions via segment mapping
[2019-09-04 18:58:56] Retrieving sequences for splices
[2019-09-04 19:00:51] Indexing splices
Building a SMALL index
[2019-09-04 19:02:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 19:04:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 19:06:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 19:08:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 19:10:53] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 19:12:50] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 19:14:11] Joining segment hits
[2019-09-04 19:23:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 19:25:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 19:28:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 19:30:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 19:32:56] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 19:35:05] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 19:36:50] Joining segment hits
[2019-09-04 19:46:45] Reporting output tracks
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[2019-09-04 20:43:20] A summary of the alignment counts can be found in /scratch/9142553.1.linga/tophat2/align_summary.txt
[2019-09-04 20:43:20] Run complete: 09:20:56 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 41 files...