[2017-06-14 21:34:42] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:43] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:43] Checking for reference FASTA file
[2017-06-14 21:34:43] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:48] Reading known junctions from GTF file
[2017-06-14 21:34:51] Preparing reads
	 left reads: min. length=101, max. length=101, 19310225 kept reads (57 discarded)
	right reads: min. length=101, max. length=101, 19261572 kept reads (48710 discarded)
[2017-06-14 21:54:51] Building transcriptome data files /scratch/9328375.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:55:07] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:56:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:10:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:23:08] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:23:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:34:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:35:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:37:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:40:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:42:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:57:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 23:00:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 23:03:17] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:07:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:11:32] Searching for junctions via segment mapping
[2017-06-14 23:22:56] Retrieving sequences for splices
[2017-06-14 23:25:29] Indexing splices
Building a SMALL index
[2017-06-14 23:26:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:27:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:28:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:29:07] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:30:01] Joining segment hits
[2017-06-14 23:33:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:35:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:36:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:37:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:38:31] Joining segment hits
[2017-06-14 23:42:49] Reporting output tracks
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[2017-06-15 00:08:28] A summary of the alignment counts can be found in /scratch/9328375.1.linga/tophat2/align_summary.txt
[2017-06-15 00:08:28] Run complete: 02:33:45 elapsed
[samopen] SAM header is present: 23 sequences.
[bam_sort_core] merging from 13 files...