I am trying to run tophat2 on a set of SE reads:
But I am getting a weird error message:
What is going on here? It seems tophat2 is looking for a file/directory when it encounters "--min-intron-length" yet I don't understand why. Can you help?
Code:
tophat2 ../../../references/genomes/xen-trop/ens71/xen-trop-4-2-71 CO1_CGATGT_L008.fastq --min-intron-length 6 --max-insertion-length 3 --max-deletion-length 3 --b2-seed 73 --solexa1.3-quals --microexon-search --num-threads 32 --library-type fr-unstranded --no-coverage-search --GTF ../../../references/gtf/xen-trop/ens71/Xenopus_tropicalis.JGI_4.2.71.gtf
Code:
[2013-08-10 14:34:22] Beginning TopHat run (v2.0.9) [2013-08-10 14:34:22] Checking for Bowtie Bowtie version: 2.1.0.0 [2013-08-10 14:34:22] Checking for Samtools Samtools version: 0.1.19.0 [2013-08-10 14:34:22] Checking for Bowtie index files (genome).. [2013-08-10 14:34:22] Checking for reference FASTA file [2013-08-10 14:34:22] Generating SAM header for ../../../references/genomes/xen-trop/ens71/xen-trop-4-2-71 Traceback (most recent call last): File "/galaxy/software/tophat2/2.0.9/tophat", line 4072, in ? sys.exit(main()) File "/galaxy/software/tophat2/2.0.9/tophat", line 3926, in main params.read_params = check_reads_format(params, reads_list) File "/galaxy/software/tophat2/2.0.9/tophat", line 1829, in check_reads_format zf = ZReader(f_name, params) File "/galaxy/software/tophat2/2.0.9/tophat", line 1782, in __init__ self.file=open(filename) IOError: [Errno 2] No such file or directory: '--min-intron-length'
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