[2018-10-13 09:52:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:52:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:52:10] Checking for Bowtie index files (genome)..
[2018-10-13 09:52:10] Checking for reference FASTA file
[2018-10-13 09:52:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:52:15] Reading known junctions from GTF file
[2018-10-13 09:52:19] Preparing reads
	 left reads: min. length=100, max. length=100, 198066 kept reads (165 discarded)
	right reads: min. length=100, max. length=100, 197878 kept reads (353 discarded)
[2018-10-13 09:52:27] Building transcriptome data files /scratch/8793159.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:52:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:00:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:01:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:01:30] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:01:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:01:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:02:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:02:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:02:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:02:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:02:55] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:03:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:03:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:03:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:03:32] Searching for junctions via segment mapping
[2018-10-13 10:06:07] Retrieving sequences for splices
[2018-10-13 10:08:07] Indexing splices
[2018-10-13 10:08:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:08:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:08:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:08:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:08:43] Joining segment hits
[2018-10-13 10:10:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:10:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:11:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:11:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:11:11] Joining segment hits
[2018-10-13 10:13:25] Reporting output tracks
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[2018-10-13 10:16:33] A summary of the alignment counts can be found in /scratch/8793159.1.linga/tophat2/align_summary.txt
[2018-10-13 10:16:33] Run complete: 00:24:22 elapsed