[2014-12-19 12:55:19] Beginning TopHat run (v2.0.9)
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[2014-12-19 12:55:19] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-12-19 12:55:19] Checking for Samtools
		Samtools version:	 0.1.18.0
[2014-12-19 12:55:19] Checking for Bowtie index files (genome)..
[2014-12-19 12:55:19] Checking for reference FASTA file
[2014-12-19 12:55:19] Generating SAM header for Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-12-19 12:55:20] Reading known junctions from GTF file
[2014-12-19 12:55:23] Preparing reads
	 left reads: min. length=101, max. length=101, 18308054 kept reads (479804 discarded)
[2014-12-19 13:02:15] Building transcriptome data files..
[2014-12-19 13:02:20] Building Bowtie index from Crassostrea_gigas.GCA_000297895.1.24.fa
[2014-12-19 13:03:03] 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 13:08:30] Resuming TopHat pipeline with unmapped reads
[2014-12-19 13:08:30] 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 13:34:23] 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 13:37:26] 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 13:40:30] 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 13:43:25] 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 13:46:20] 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 13:49:11] Searching for junctions via segment mapping
[2014-12-19 13:51:33] Retrieving sequences for splices
[2014-12-19 13:51:54] Indexing splices
[2014-12-19 13:52:32] 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 13:53:32] 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 13:54:32] 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 13:55:31] 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 13:56:30] 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 13:57:27] Joining segment hits
[2014-12-19 14:00:09] Reporting output tracks
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[2014-12-19 14:08:31] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2014-12-19 14:08:31] Run complete: 01:13:11 elapsed