[2018-10-13 02:24:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:24:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:24:08] Checking for Bowtie index files (genome)..
[2018-10-13 02:24:08] Checking for reference FASTA file
[2018-10-13 02:24:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:24:13] Reading known junctions from GTF file
[2018-10-13 02:24:17] Preparing reads
	 left reads: min. length=100, max. length=100, 441532 kept reads (260 discarded)
	right reads: min. length=100, max. length=100, 441031 kept reads (761 discarded)
[2018-10-13 02:24:35] Building transcriptome data files /scratch/8792915.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:24:53] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:33:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:33:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:34:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:34:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:35:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:35:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:35:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:35:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:35:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:36:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:36:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:36:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:37:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:37:18] Searching for junctions via segment mapping
[2018-10-13 02:40:04] Retrieving sequences for splices
[2018-10-13 02:42:11] Indexing splices
[2018-10-13 02:42:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:42:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:42:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:42:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:42:50] Joining segment hits
[2018-10-13 02:45:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:45:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:45:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:45:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:45:29] Joining segment hits
[2018-10-13 02:47:55] Reporting output tracks
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[2018-10-13 02:51:43] A summary of the alignment counts can be found in /scratch/8792915.1.linga/tophat2/align_summary.txt
[2018-10-13 02:51:43] Run complete: 00:27:34 elapsed