[2018-10-13 05:32:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:32:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:32:17] Checking for Bowtie index files (genome)..
[2018-10-13 05:32:17] Checking for reference FASTA file
[2018-10-13 05:32:17] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:32:18] Reading known junctions from GTF file
[2018-10-13 05:32:21] Preparing reads
	 left reads: min. length=100, max. length=100, 731392 kept reads (151 discarded)
	right reads: min. length=100, max. length=100, 731213 kept reads (330 discarded)
[2018-10-13 05:32:42] Building transcriptome data files /scratch/8793027.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:32:53] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:38:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:39:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:39:47] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:39:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:40:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:40:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:40:16] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:40:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:40:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:40:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:40:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:40:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:41:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:41:09] Searching for junctions via segment mapping
[2018-10-13 05:43:39] Retrieving sequences for splices
[2018-10-13 05:44:52] Indexing splices
[2018-10-13 05:45:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:45:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:45:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:45:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:45:17] Joining segment hits
[2018-10-13 05:46:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:46:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:46:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:46:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:46:52] Joining segment hits
[2018-10-13 05:48:13] Reporting output tracks
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[2018-10-13 05:54:23] A summary of the alignment counts can be found in /scratch/8793027.1.c/tophat2/align_summary.txt
[2018-10-13 05:54:23] Run complete: 00:22:06 elapsed