[2018-10-12 22:38:28] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:38:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:38:28] Checking for Bowtie index files (genome)..
[2018-10-12 22:38:28] Checking for reference FASTA file
[2018-10-12 22:38:28] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:38:33] Reading known junctions from GTF file
[2018-10-12 22:38:38] Preparing reads
	 left reads: min. length=100, max. length=100, 443816 kept reads (279 discarded)
	right reads: min. length=100, max. length=100, 443489 kept reads (606 discarded)
[2018-10-12 22:38:57] Building transcriptome data files /scratch/8792805.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:39:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:48:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:49:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:49:46] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:49:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:50:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:50:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:50:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:50:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:51:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:51:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:52:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:52:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:52:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:52:38] Searching for junctions via segment mapping
[2018-10-12 22:55:27] Retrieving sequences for splices
[2018-10-12 22:57:39] Indexing splices
[2018-10-12 22:58:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:58:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:58:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:58:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:58:19] Joining segment hits
[2018-10-12 23:00:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:00:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:01:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:01:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:01:09] Joining segment hits
[2018-10-12 23:03:42] Reporting output tracks
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[2018-10-12 23:07:22] A summary of the alignment counts can be found in /scratch/8792805.1.linga/tophat2/align_summary.txt
[2018-10-12 23:07:22] Run complete: 00:28:53 elapsed