[2013-03-05 08:38:38] Beginning TopHat run (v2.0.5)
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[2013-03-05 08:38:38] Checking for Bowtie
		  Bowtie version:	 2.0.0.7
[2013-03-05 08:38:38] Checking for Samtools
		Samtools version:	 0.1.18.0
[2013-03-05 08:38:38] Checking for Bowtie index files
[2013-03-05 08:38:38] Checking for reference FASTA file
[2013-03-05 08:38:38] Generating SAM header for oyster.v9_90
Warning: found a read < 20bp in solid0078_20091105_DH3.fastq
Warning: found a read < 20bp in solid0078_20091105_DH3.fastq
Warning: found a read < 20bp in solid0078_20091105_DH3.fastq
Warning: found a read < 20bp in solid0078_20091105_DH3.fastq
	format:		 fastq
	quality scale:	 phred33 (default)
[2013-03-05 08:38:45] Reading known junctions from GTF file
[2013-03-05 08:38:46] Preparing reads
	 left reads: min. length=12, max. length=51, 39388836 kept reads (268199 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped to too many places
[2013-03-05 08:46:15] Creating transcriptome data files..
[2013-03-05 08:46:19] Building Bowtie index from gffread_filtered.fa
[2013-03-05 08:47:04] Mapping left_kept_reads to transcriptome gffread_filtered with Bowtie2 
/usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering)
/usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx)
[2013-03-05 08:53:11] Resuming TopHat pipeline with unmapped reads
[2013-03-05 08:53:11] Mapping left_kept_reads.m2g_um to genome oyster.v9_90 with Bowtie2 
/usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx)
/usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering)
/usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx)
[2013-03-05 09:22:14] Mapping left_kept_reads.m2g_um_seg1 to genome oyster.v9_90 with Bowtie2 (1/2)
/usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering)
[2013-03-05 09:30:26] Mapping left_kept_reads.m2g_um_seg2 to genome oyster.v9_90 with Bowtie2 (2/2)
/usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering)
[2013-03-05 09:57:26] Searching for junctions via segment mapping
[2013-03-06 01:34:49] Retrieving sequences for splices
[2013-03-06 01:35:40] Indexing splices
[2013-03-06 01:48:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
/usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering)
[2013-03-06 01:58:45] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
/usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering: /lib64/libz.so.1: no version information available (required by /usr/local2/tophat-2.0.5.Linux_x86_64/fix_map_ordering)
[2013-03-06 02:25:40] Joining segment hits
[2013-03-06 02:26:57] Reporting output tracks
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[2013-03-06 02:34:13] Run complete: 17:55:34 elapsed