[2018-10-13 03:46:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:46:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:46:08] Checking for Bowtie index files (genome)..
[2018-10-13 03:46:08] Checking for reference FASTA file
[2018-10-13 03:46:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:46:13] Reading known junctions from GTF file
[2018-10-13 03:46:17] Preparing reads
	 left reads: min. length=100, max. length=100, 215900 kept reads (139 discarded)
	right reads: min. length=100, max. length=100, 215571 kept reads (468 discarded)
[2018-10-13 03:46:26] Building transcriptome data files /scratch/8792970.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:46:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:54:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:54:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:55:12] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:55:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:55:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:55:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:55:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:56:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:56:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:56:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:56:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:56:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:56:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:57:07] Searching for junctions via segment mapping
[2018-10-13 03:59:47] Retrieving sequences for splices
[2018-10-13 04:01:55] Indexing splices
[2018-10-13 04:02:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:02:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:02:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:02:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:02:32] Joining segment hits
[2018-10-13 04:04:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:04:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:04:59] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:05:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:05:07] Joining segment hits
[2018-10-13 04:07:41] Reporting output tracks
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[2018-10-13 04:10:53] A summary of the alignment counts can be found in /scratch/8792970.1.linga/tophat2/align_summary.txt
[2018-10-13 04:10:53] Run complete: 00:24:44 elapsed