[2018-10-13 18:38:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:38:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:38:57] Checking for Bowtie index files (genome)..
[2018-10-13 18:38:57] Checking for reference FASTA file
[2018-10-13 18:38:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:39:01] Reading known junctions from GTF file
[2018-10-13 18:39:05] Preparing reads
	 left reads: min. length=100, max. length=100, 365385 kept reads (170 discarded)
	right reads: min. length=100, max. length=100, 365140 kept reads (415 discarded)
[2018-10-13 18:39:20] Building transcriptome data files /scratch/8793448.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:39:39] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:47:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:47:40] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:48:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:48:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:48:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:48:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:49:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:49:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:49:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:49:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:50:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:50:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:50:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:50:37] Searching for junctions via segment mapping
[2018-10-13 18:53:11] Retrieving sequences for splices
[2018-10-13 18:55:19] Indexing splices
[2018-10-13 18:55:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:55:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:55:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:55:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:55:55] Joining segment hits
[2018-10-13 18:58:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:58:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:58:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:58:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:58:29] Joining segment hits
[2018-10-13 19:01:01] Reporting output tracks
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[2018-10-13 19:04:10] A summary of the alignment counts can be found in /scratch/8793448.1.linga/tophat2/align_summary.txt
[2018-10-13 19:04:10] Run complete: 00:25:12 elapsed