[2019-09-04 11:17:20] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:17:20] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:17:21] Checking for Bowtie index files (genome)..
[2019-09-04 11:17:21] Checking for reference FASTA file
[2019-09-04 11:17:21] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:17:26] Reading known junctions from GTF file
[2019-09-04 11:17:29] Preparing reads
	 left reads: min. length=150, max. length=150, 28256327 kept reads (12 discarded)
	right reads: min. length=150, max. length=150, 28255290 kept reads (1049 discarded)
[2019-09-04 11:44:54] Building transcriptome data files /scratch/9142558.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:45:15] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:53:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:13:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:34:00] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:34:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:11:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:17:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 13:24:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 13:30:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 13:35:49] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:40:41] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:43:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:21:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 14:27:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:33:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:40:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:46:32] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:52:14] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:55:24] Searching for junctions via segment mapping
[2019-09-04 15:16:38] Retrieving sequences for splices
[2019-09-04 15:18:32] Indexing splices
Building a SMALL index
[2019-09-04 15:19:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 15:21:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 15:22:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 15:24:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 15:26:39] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 15:28:08] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 15:29:09] Joining segment hits
[2019-09-04 15:36:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 15:38:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 15:40:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 15:42:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 15:44:02] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 15:45:54] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 15:47:15] Joining segment hits
[2019-09-04 15:56:01] Reporting output tracks
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[2019-09-04 16:36:17] A summary of the alignment counts can be found in /scratch/9142558.1.linga/tophat2/align_summary.txt
[2019-09-04 16:36:17] Run complete: 05:18:56 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 30 files...