[2018-10-13 04:49:02] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:49:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:49:02] Checking for Bowtie index files (genome)..
[2018-10-13 04:49:02] Checking for reference FASTA file
[2018-10-13 04:49:02] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:49:06] Reading known junctions from GTF file
[2018-10-13 04:49:11] Preparing reads
	 left reads: min. length=100, max. length=100, 413775 kept reads (34 discarded)
	right reads: min. length=100, max. length=100, 413690 kept reads (119 discarded)
[2018-10-13 04:49:31] Building transcriptome data files /scratch/8793004.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:49:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:58:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:58:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:59:04] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:59:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:59:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:59:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:59:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:59:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:00:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:00:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:00:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:00:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:00:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:00:59] Searching for junctions via segment mapping
[2018-10-13 05:04:05] Retrieving sequences for splices
[2018-10-13 05:06:14] Indexing splices
[2018-10-13 05:06:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:06:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:06:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:06:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:06:52] Joining segment hits
[2018-10-13 05:09:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:09:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:09:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:09:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:09:25] Joining segment hits
[2018-10-13 05:11:40] Reporting output tracks
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[2018-10-13 05:15:38] A summary of the alignment counts can be found in /scratch/8793004.1.linga/tophat2/align_summary.txt
[2018-10-13 05:15:38] Run complete: 00:26:35 elapsed