[2013-03-04 13:35:05] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2013-03-04 13:35:05] Checking for Bowtie
		  Bowtie version:	 2.0.0.7
[2013-03-04 13:35:05] Checking for Samtools
		Samtools version:	 0.1.18.0
[2013-03-04 13:35:13] Checking for Bowtie index files
[2013-03-04 13:35:13] Checking for reference FASTA file
[2013-03-04 13:35:13] Generating SAM header for oyster.v9_90
Warning: found a read < 20bp in solid0078_20091105_BB3.fastq
Warning: found a read < 20bp in solid0078_20091105_BB3.fastq
Warning: found a read < 20bp in solid0078_20091105_BB3.fastq
Warning: found a read < 20bp in solid0078_20091105_BB3.fastq
	format:		 fastq
	quality scale:	 phred33 (default)
[2013-03-04 13:35:14] Reading known junctions from GTF file
[2013-03-04 13:35:15] Preparing reads
	 left reads: min. length=12, max. length=51, 37814786 kept reads (5675804 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
[2013-03-04 13:41:34] Creating transcriptome data files..
[2013-03-04 13:41:39] Building Bowtie index from gffread_filtered.fa
[2013-03-04 13:42:23] Mapping left_kept_reads to transcriptome gffread_filtered 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)
[2013-03-04 13:48:47] Resuming TopHat pipeline with unmapped reads
[2013-03-04 13:48:47] 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)
[2013-03-04 14:19:16] 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)
[2013-03-04 14:28:12] 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)
[2013-03-04 14:54:25] Searching for junctions via segment mapping
[2013-03-05 07:32:07] Retrieving sequences for splices
[2013-03-05 07:32:59] Indexing splices
[2013-03-05 07:45:31] 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)
[2013-03-05 07:58:53] 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)
[2013-03-05 08:28:04] Joining segment hits
[2013-03-05 08:29:37] Reporting output tracks
-----------------------------------------------
[2013-03-05 08:38:37] Run complete: 19:03:32 elapsed