[2014-02-05 18:18:28] Beginning TopHat run (v2.0.9)
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[2014-02-05 18:18:28] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-02-05 18:18:28] Checking for Samtools
		Samtools version:	 0.1.18.0
[2014-02-05 18:18:28] Checking for Bowtie index files (genome)..
[2014-02-05 18:18:28] Checking for reference FASTA file
[2014-02-05 18:18:28] Generating SAM header for Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-02-05 18:18:52] Reading known junctions from GTF file
[2014-02-05 18:18:56] Preparing reads
	 left reads: min. length=49, max. length=49, 12520524 kept reads (482 discarded)
[2014-02-05 18:26:32] Building transcriptome data files..
[2014-02-05 18:26:38] Building Bowtie index from Crassostrea_gigas.GCA_000297895.1.21.fa
[2014-02-05 18:27:43] Mapping left_kept_reads to transcriptome Crassostrea_gigas.GCA_000297895.1.21 with Bowtie2 
/usr/local2/tophat-2.0.9.Linux_x86_64/bam2fastx: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/bam2fastx)
/usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering)
[2014-02-05 18:31:40] Resuming TopHat pipeline with unmapped reads
[2014-02-05 18:31:40] Mapping left_kept_reads.m2g_um to genome Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel with Bowtie2 
/usr/local2/tophat-2.0.9.Linux_x86_64/bam2fastx: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/bam2fastx)
/usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering)
/usr/local2/tophat-2.0.9.Linux_x86_64/bam2fastx: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/bam2fastx)
[2014-02-05 18:35:25] Mapping left_kept_reads.m2g_um_seg1 to genome Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel with Bowtie2 (1/2)
/usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering)
[2014-02-05 18:36:36] Mapping left_kept_reads.m2g_um_seg2 to genome Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel with Bowtie2 (2/2)
/usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering)
[2014-02-05 18:38:10] Searching for junctions via segment mapping
[2014-02-05 18:53:56] Retrieving sequences for splices
[2014-02-05 18:54:29] Indexing splices
[2014-02-05 18:57:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
/usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering)
[2014-02-05 18:59:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
/usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.9.Linux_x86_64/fix_map_ordering)
[2014-02-05 19:01:59] Joining segment hits
[2014-02-05 19:02:45] Reporting output tracks
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[2014-02-05 19:08:03] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2014-02-05 19:08:03] Run complete: 00:49:34 elapsed