[2018-10-13 02:16:26] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:16:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:16:26] Checking for Bowtie index files (genome)..
[2018-10-13 02:16:26] Checking for reference FASTA file
[2018-10-13 02:16:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:16:31] Reading known junctions from GTF file
[2018-10-13 02:16:35] Preparing reads
	 left reads: min. length=100, max. length=100, 129686 kept reads (205 discarded)
	right reads: min. length=100, max. length=100, 129564 kept reads (327 discarded)
[2018-10-13 02:16:41] Building transcriptome data files /scratch/8792909.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:17:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:25:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:25:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:26:14] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:26:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:26:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:26:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:26:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:27:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:27:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:27:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:27:43] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:27:54] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:28:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:28:12] Searching for junctions via segment mapping
[2018-10-13 02:30:28] Retrieving sequences for splices
[2018-10-13 02:32:27] Indexing splices
[2018-10-13 02:32:46] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:32:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:32:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:32:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:33:02] Joining segment hits
[2018-10-13 02:35:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:35:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:35:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:35:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:35:22] Joining segment hits
[2018-10-13 02:37:46] Reporting output tracks
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[2018-10-13 02:40:15] A summary of the alignment counts can be found in /scratch/8792909.1.linga/tophat2/align_summary.txt
[2018-10-13 02:40:15] Run complete: 00:23:48 elapsed