[2015-03-16 22:15:04] Beginning TopHat run (v2.0.13)
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[2015-03-16 22:15:04] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-03-16 22:15:04] Checking for Bowtie index files (transcriptome)..
[2015-03-16 22:15:04] Checking for Bowtie index files (genome)..
[2015-03-16 22:15:04] Checking for reference FASTA file
[2015-03-16 22:15:04] Generating SAM header for /Volumes/Data/Sam/fish546_2015/gigasHSrnaSeq/raw_data/Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome
[2015-03-16 22:15:06] Reading known junctions from GTF file
[2015-03-16 22:15:12] Preparing reads
	 left reads: min. length=22, max. length=22, 35978803 kept reads (6945 discarded)
[2015-03-16 22:25:16] Using pre-built transcriptome data..
[2015-03-16 22:25:23] Mapping left_kept_reads to transcriptome Crassostrea_gigas.GCA_000297895.1.24 with Bowtie2 
[2015-03-16 22:32:43] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
	If the read length is greater than or equal to 45bp,
	we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2015-03-16 22:32:44] Mapping left_kept_reads.m2g_um to genome Crassostrea_gigas.GCA_000297895.1.24.dna_sm.genome with Bowtie2 
[2015-03-16 22:39:34] Searching for junctions via segment mapping
[2015-03-16 22:58:48] Retrieving sequences for splices
[2015-03-16 23:00:05] Indexing splices
[2015-03-16 23:11:46] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/tmp/left_kept_reads.m2g_um_unmapped.bam
[2015-03-16 23:17:32] Joining segment hits
[2015-03-16 23:23:11] Reporting output tracks
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[2015-03-16 23:31:22] A summary of the alignment counts can be found in /Volumes/web-1/scaphapoda/Collin/O_lurida/analysis/tophat_larvae/align_summary.txt
[2015-03-16 23:31:22] Run complete: 01:16:18 elapsed