[2018-10-13 09:26:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:26:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:26:09] Checking for Bowtie index files (genome)..
[2018-10-13 09:26:09] Checking for reference FASTA file
[2018-10-13 09:26:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:26:11] Reading known junctions from GTF file
[2018-10-13 09:26:14] Preparing reads
	 left reads: min. length=100, max. length=100, 2855494 kept reads (366 discarded)
	right reads: min. length=100, max. length=100, 2854548 kept reads (1312 discarded)
[2018-10-13 09:27:36] Building transcriptome data files /scratch/8793144.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:27:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:33:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:34:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:35:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:35:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:36:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:36:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:36:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:36:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:37:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:37:53] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:38:02] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:38:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:38:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:38:38] Searching for junctions via segment mapping
[2018-10-13 09:41:40] Retrieving sequences for splices
[2018-10-13 09:42:53] Indexing splices
Building a SMALL index
[2018-10-13 09:43:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:43:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:43:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:43:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:43:20] Joining segment hits
[2018-10-13 09:44:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:44:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:44:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:44:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:45:00] Joining segment hits
[2018-10-13 09:46:25] Reporting output tracks
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[2018-10-13 09:55:28] A summary of the alignment counts can be found in /scratch/8793144.1.c/tophat2/align_summary.txt
[2018-10-13 09:55:28] Run complete: 00:29:19 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...