any ideas?
Code:
matthew@macmanes:~/tophat-1.3.0$ /home/matthew/tophat-1.3.0/tophat -o /media/hd/annotation/tophat/solitary -r 100 -p 16 /media/hd/annotation/tophat/bowtie.index/tuco.mrna.annotate.2June11 /media/hd/tuco/mrna/peruanus/clipped/cp.final.clip_1.fq /media/hd/tuco/mrna/peruanus/clipped/cp.final.clip_2.fq [Thu Jun 2 17:47:45 2011] Beginning TopHat run (v1.3.0) ----------------------------------------------- [Thu Jun 2 17:47:45 2011] Preparing output location /media/hd/annotation/tophat/solitary/ [Thu Jun 2 17:47:45 2011] Checking for Bowtie index files [Thu Jun 2 17:47:45 2011] Checking for reference FASTA file [Thu Jun 2 17:47:45 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Thu Jun 2 17:47:45 2011] Checking for Samtools Samtools Version: 0.1.16 [Thu Jun 2 17:47:45 2011] Generating SAM header for /media/hd/annotation/tophat/bowtie.index/tuco.mrna.annotate.2June11 [Thu Jun 2 17:47:49 2011] Preparing reads format: fastq quality scale: phred33 (default) Traceback (most recent call last): File "/home/matthew/tophat-1.3.0/tophat", line 2584, in <module> sys.exit(main()) File "/home/matthew/tophat-1.3.0/tophat", line 2511, in main "left_kept_reads", "Left ") File "/home/matthew/tophat-1.3.0/tophat", line 1362, in prep_reads shell_cmd = ' '.join(filter_cmd) TypeError: sequence item 50: expected string, NoneType found
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