[2019-09-04 11:20:35] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:20:35] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:20:35] Checking for Bowtie index files (genome)..
[2019-09-04 11:20:35] Checking for reference FASTA file
[2019-09-04 11:20:35] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:20:40] Reading known junctions from GTF file
[2019-09-04 11:20:43] Preparing reads
	 left reads: min. length=150, max. length=150, 30640343 kept reads (15 discarded)
	right reads: min. length=150, max. length=150, 30639227 kept reads (1131 discarded)
[2019-09-04 11:49:45] Building transcriptome data files /scratch/9142566.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:50:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:57:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:02:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:54:31] Resuming TopHat pipeline with unmapped reads
[2019-09-04 13:54:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:54:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:04:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:14:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:25:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:36:25] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:44:55] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:49:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 16:49:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 16:58:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 17:07:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 17:17:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 17:27:38] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 17:36:12] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 17:40:58] Searching for junctions via segment mapping
[2019-09-04 17:58:03] Retrieving sequences for splices
[2019-09-04 18:00:03] Indexing splices
Building a SMALL index
[2019-09-04 18:01:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 18:04:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 18:06:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 18:09:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 18:12:25] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 18:14:56] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 18:16:12] Joining segment hits
[2019-09-04 18:25:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 18:27:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 18:28:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 18:30:38] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 18:32:53] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 18:35:09] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 18:37:05] Joining segment hits
[2019-09-04 18:45:00] Reporting output tracks
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[2019-09-04 19:21:10] A summary of the alignment counts can be found in /scratch/9142566.1.linga/tophat2/align_summary.txt
[2019-09-04 19:21:10] Run complete: 08:00:35 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 33 files...