[2018-10-13 04:30:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:30:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:30:56] Checking for Bowtie index files (genome)..
[2018-10-13 04:30:56] Checking for reference FASTA file
[2018-10-13 04:30:56] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:31:01] Reading known junctions from GTF file
[2018-10-13 04:31:05] Preparing reads
	 left reads: min. length=100, max. length=100, 984899 kept reads (81 discarded)
	right reads: min. length=100, max. length=100, 984342 kept reads (638 discarded)
[2018-10-13 04:31:48] Building transcriptome data files /scratch/8792994.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:32:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:40:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:41:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:42:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:42:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:42:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:42:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:43:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:43:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:43:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:44:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:44:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:44:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:44:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:44:52] Searching for junctions via segment mapping
[2018-10-13 04:48:53] Retrieving sequences for splices
[2018-10-13 04:51:00] Indexing splices
[2018-10-13 04:51:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:51:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:51:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:51:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:51:46] Joining segment hits
[2018-10-13 04:54:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:54:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:54:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:54:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:54:56] Joining segment hits
[2018-10-13 04:57:51] Reporting output tracks
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[2018-10-13 05:10:31] A summary of the alignment counts can be found in /scratch/8792994.1.linga/tophat2/align_summary.txt
[2018-10-13 05:10:31] Run complete: 00:39:35 elapsed