[2018-10-13 01:48:26] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:48:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:48:26] Checking for Bowtie index files (genome)..
[2018-10-13 01:48:26] Checking for reference FASTA file
[2018-10-13 01:48:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:48:30] Reading known junctions from GTF file
[2018-10-13 01:48:35] Preparing reads
	 left reads: min. length=100, max. length=100, 116740 kept reads (62 discarded)
	right reads: min. length=100, max. length=100, 116660 kept reads (142 discarded)
[2018-10-13 01:48:40] Building transcriptome data files /scratch/8792896.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:49:01] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:57:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:57:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:58:04] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:58:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:58:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:58:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:58:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:58:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:58:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:59:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:59:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:59:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:59:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:59:49] Searching for junctions via segment mapping
[2018-10-13 02:02:15] Retrieving sequences for splices
[2018-10-13 02:04:26] Indexing splices
[2018-10-13 02:04:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:04:52] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:04:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:05:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:05:04] Joining segment hits
[2018-10-13 02:07:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:07:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:07:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:07:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:07:35] Joining segment hits
[2018-10-13 02:09:50] Reporting output tracks
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[2018-10-13 02:12:24] A summary of the alignment counts can be found in /scratch/8792896.1.linga/tophat2/align_summary.txt
[2018-10-13 02:12:24] Run complete: 00:23:58 elapsed