[2018-10-13 05:44:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:44:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:44:08] Checking for Bowtie index files (genome)..
[2018-10-13 05:44:08] Checking for reference FASTA file
[2018-10-13 05:44:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:44:10] Reading known junctions from GTF file
[2018-10-13 05:44:12] Preparing reads
	 left reads: min. length=100, max. length=100, 557547 kept reads (1504 discarded)
	right reads: min. length=100, max. length=100, 557323 kept reads (1728 discarded)
[2018-10-13 05:44:28] Building transcriptome data files /scratch/8793034.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:44:38] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:49:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:49:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:50:32] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:50:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:50:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:51:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:51:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:51:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:51:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:51:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:51:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:52:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:52:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:52:14] Searching for junctions via segment mapping
[2018-10-13 05:54:39] Retrieving sequences for splices
[2018-10-13 05:55:47] Indexing splices
[2018-10-13 05:55:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:56:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:56:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:56:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:56:09] Joining segment hits
[2018-10-13 05:57:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:57:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:57:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:57:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:57:36] Joining segment hits
[2018-10-13 05:58:52] Reporting output tracks
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[2018-10-13 06:01:42] A summary of the alignment counts can be found in /scratch/8793034.1.p16/tophat2/align_summary.txt
[2018-10-13 06:01:42] Run complete: 00:17:34 elapsed