[2019-09-04 11:17:30] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:17:30] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:17:31] Checking for Bowtie index files (genome)..
[2019-09-04 11:17:31] Checking for reference FASTA file
[2019-09-04 11:17:31] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:17:34] Reading known junctions from GTF file
[2019-09-04 11:17:37] Preparing reads
	 left reads: min. length=150, max. length=150, 29623880 kept reads (10 discarded)
	right reads: min. length=150, max. length=150, 29622698 kept reads (1192 discarded)
[2019-09-04 11:38:09] Building transcriptome data files /scratch/9142557.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:38:18] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:43:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 11:56:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:09:39] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:09:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 12:34:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 12:38:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 12:42:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 12:46:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 12:50:43] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 12:54:09] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 12:56:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:23:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:27:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 13:31:54] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 13:35:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 13:39:58] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:43:52] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:46:11] Searching for junctions via segment mapping
[2019-09-04 13:58:39] Retrieving sequences for splices
[2019-09-04 13:59:42] Indexing splices
Building a SMALL index
[2019-09-04 14:00:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:01:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:02:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:03:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:04:09] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:04:59] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:05:34] Joining segment hits
[2019-09-04 14:09:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:10:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:11:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:12:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:13:02] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:13:56] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:14:38] Joining segment hits
[2019-09-04 14:17:54] Reporting output tracks
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[2019-09-04 14:39:24] A summary of the alignment counts can be found in /scratch/9142557.1.linga/tophat2/align_summary.txt
[2019-09-04 14:39:24] Run complete: 03:21:53 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 31 files...