[2018-10-13 01:16:46] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:16:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:16:46] Checking for Bowtie index files (genome)..
[2018-10-13 01:16:46] Checking for reference FASTA file
[2018-10-13 01:16:46] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:16:51] Reading known junctions from GTF file
[2018-10-13 01:16:55] Preparing reads
	 left reads: min. length=100, max. length=100, 342035 kept reads (161 discarded)
	right reads: min. length=100, max. length=100, 341809 kept reads (387 discarded)
[2018-10-13 01:17:11] Building transcriptome data files /scratch/8792880.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:17:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:26:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:26:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:27:47] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:27:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:28:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:28:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:28:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:29:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:29:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:29:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:30:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:30:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:30:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:30:35] Searching for junctions via segment mapping
[2018-10-13 01:33:18] Retrieving sequences for splices
[2018-10-13 01:35:30] Indexing splices
[2018-10-13 01:35:54] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:35:58] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:36:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:36:08] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:36:13] Joining segment hits
[2018-10-13 01:38:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:38:43] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:38:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:38:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:38:58] Joining segment hits
[2018-10-13 01:41:18] Reporting output tracks
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[2018-10-13 01:44:44] A summary of the alignment counts can be found in /scratch/8792880.1.linga/tophat2/align_summary.txt
[2018-10-13 01:44:44] Run complete: 00:27:57 elapsed