[2018-10-13 01:48:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:48:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:48:09] Checking for Bowtie index files (genome)..
[2018-10-13 01:48:09] Checking for reference FASTA file
[2018-10-13 01:48:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:48:11] Reading known junctions from GTF file
[2018-10-13 01:48:13] Preparing reads
	 left reads: min. length=100, max. length=100, 323002 kept reads (203 discarded)
	right reads: min. length=100, max. length=100, 322463 kept reads (742 discarded)
[2018-10-13 01:48:23] Building transcriptome data files /scratch/8792898.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:48:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:53:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:54:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:54:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:54:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:54:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:55:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:55:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:55:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:55:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:55:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:55:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:55:46] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:55:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:55:57] Searching for junctions via segment mapping
[2018-10-13 01:57:22] Retrieving sequences for splices
[2018-10-13 01:58:34] Indexing splices
[2018-10-13 01:58:46] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:58:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:58:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:58:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:58:56] Joining segment hits
[2018-10-13 02:00:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:00:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:00:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:00:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:00:27] Joining segment hits
[2018-10-13 02:01:48] Reporting output tracks
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[2018-10-13 02:03:34] A summary of the alignment counts can be found in /scratch/8792898.1.c/tophat2/align_summary.txt
[2018-10-13 02:03:34] Run complete: 00:15:24 elapsed