[2014-12-19 10:11:39] Beginning TopHat run (v2.0.9)
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[2014-12-19 10:11:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-12-19 10:11:39] Checking for Samtools
		Samtools version:	 0.1.18.0
[2014-12-19 10:11:39] Checking for Bowtie index files (genome)..
[2014-12-19 10:11:39] Checking for reference FASTA file
[2014-12-19 10:11:39] Generating SAM header for Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-12-19 10:11:40] Reading known junctions from GTF file
[2014-12-19 10:11:42] Preparing reads
	 left reads: min. length=101, max. length=101, 22797322 kept reads (17404 discarded)
[2014-12-19 10:20:15] Building transcriptome data files..
[2014-12-19 10:20:19] Building Bowtie index from Crassostrea_gigas.GCA_000297895.1.24.fa
[2014-12-19 10:21:02] Mapping left_kept_reads to transcriptome Crassostrea_gigas.GCA_000297895.1.24 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)
[2014-12-19 10:29:13] Resuming TopHat pipeline with unmapped reads
[2014-12-19 10:29:13] Mapping left_kept_reads.m2g_um to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.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)
[2014-12-19 10:53:57] Mapping left_kept_reads.m2g_um_seg1 to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel with Bowtie2 (1/5)
/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)
[2014-12-19 10:56:50] Mapping left_kept_reads.m2g_um_seg2 to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel with Bowtie2 (2/5)
/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)
[2014-12-19 10:59:50] Mapping left_kept_reads.m2g_um_seg3 to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel with Bowtie2 (3/5)
/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)
[2014-12-19 11:02:47] Mapping left_kept_reads.m2g_um_seg4 to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel with Bowtie2 (4/5)
/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)
[2014-12-19 11:05:44] Mapping left_kept_reads.m2g_um_seg5 to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel with Bowtie2 (5/5)
/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)
[2014-12-19 11:08:39] Searching for junctions via segment mapping
[2014-12-19 11:11:33] Retrieving sequences for splices
[2014-12-19 11:11:54] Indexing splices
[2014-12-19 11:12:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/5)
/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)
[2014-12-19 11:14:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/5)
/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)
[2014-12-19 11:15:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/5)
/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)
[2014-12-19 11:16:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/5)
/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)
[2014-12-19 11:17:56] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/5)
/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)
[2014-12-19 11:19:11] Joining segment hits
[2014-12-19 11:21:56] Reporting output tracks
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[2014-12-19 11:32:31] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2014-12-19 11:32:31] Run complete: 01:20:52 elapsed