[2014-12-19 11:32:49] Beginning TopHat run (v2.0.9)
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[2014-12-19 11:32:49] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-12-19 11:32:49] Checking for Samtools
		Samtools version:	 0.1.18.0
[2014-12-19 11:32:49] Checking for Bowtie index files (genome)..
[2014-12-19 11:32:49] Checking for reference FASTA file
[2014-12-19 11:32:49] Generating SAM header for Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-12-19 11:32:50] Reading known junctions from GTF file
[2014-12-19 11:32:52] Preparing reads
	 left reads: min. length=101, max. length=101, 23807053 kept reads (88171 discarded)
[2014-12-19 11:40:33] Building transcriptome data files..
[2014-12-19 11:40:37] Building Bowtie index from Crassostrea_gigas.GCA_000297895.1.24.fa
[2014-12-19 11:41:20] 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 11:48:43] Resuming TopHat pipeline with unmapped reads
[2014-12-19 11:48:43] 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 12:13:31] 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 12:16:40] 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 12:19:53] 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 12:23:03] 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 12:26:12] 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 12:29:20] Searching for junctions via segment mapping
[2014-12-19 12:32:29] Retrieving sequences for splices
[2014-12-19 12:32:51] Indexing splices
[2014-12-19 12:33:47] 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 12:35:10] 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 12:36:36] 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 12:38:03] 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 12:39:26] 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 12:40:51] Joining segment hits
[2014-12-19 12:44:11] Reporting output tracks
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[2014-12-19 12:55:02] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2014-12-19 12:55:02] Run complete: 01:22:12 elapsed