[2019-09-04 11:14:43] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:14:43] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:14:44] Checking for Bowtie index files (genome)..
[2019-09-04 11:14:44] Checking for reference FASTA file
[2019-09-04 11:14:44] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:14:48] Reading known junctions from GTF file
[2019-09-04 11:14:52] Preparing reads
	 left reads: min. length=150, max. length=150, 30022584 kept reads (10 discarded)
	right reads: min. length=150, max. length=150, 30021391 kept reads (1203 discarded)
[2019-09-04 11:42:02] Building transcriptome data files /scratch/9142561.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:42:21] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:49:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:22:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:55:21] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:55:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:48:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:57:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:06:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:15:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:24:57] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:32:14] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:36:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 15:29:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:38:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:47:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:57:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 16:07:15] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 16:15:58] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 16:20:47] Searching for junctions via segment mapping
[2019-09-04 16:43:25] Retrieving sequences for splices
[2019-09-04 16:45:35] Indexing splices
Building a SMALL index
[2019-09-04 16:46:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 16:48:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 16:51:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 16:53:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 16:56:05] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 16:58:15] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 16:59:41] Joining segment hits
[2019-09-04 17:08:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:10:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:13:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:15:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:18:23] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:20:55] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:22:59] Joining segment hits
[2019-09-04 17:33:21] Reporting output tracks
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[2019-09-04 18:17:41] A summary of the alignment counts can be found in /scratch/9142561.1.linga/tophat2/align_summary.txt
[2019-09-04 18:17:41] Run complete: 07:02:58 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 31 files...