[2018-10-13 02:38:07] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:38:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:38:07] Checking for Bowtie index files (genome)..
[2018-10-13 02:38:07] Checking for reference FASTA file
[2018-10-13 02:38:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:38:14] Reading known junctions from GTF file
[2018-10-13 02:38:19] Preparing reads
	 left reads: min. length=100, max. length=100, 319044 kept reads (221 discarded)
	right reads: min. length=100, max. length=100, 318686 kept reads (579 discarded)
[2018-10-13 02:38:38] Building transcriptome data files /scratch/8792920.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:38:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:48:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:48:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:49:22] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:49:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:50:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:50:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:50:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:50:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:50:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:51:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:51:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:52:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:52:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:52:36] Searching for junctions via segment mapping
[2018-10-13 02:55:20] Retrieving sequences for splices
[2018-10-13 02:58:06] Indexing splices
[2018-10-13 02:58:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:58:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:58:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:58:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:58:50] Joining segment hits
[2018-10-13 03:01:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:01:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:01:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:01:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:01:54] Joining segment hits
[2018-10-13 03:05:58] Reporting output tracks
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[2018-10-13 03:10:17] A summary of the alignment counts can be found in /scratch/8792920.1.linga/tophat2/align_summary.txt
[2018-10-13 03:10:17] Run complete: 00:32:09 elapsed