kevin@kevin-HP-Z820-Workstation:~/dev|
⇒  python ecoli_serotyping-fork/src/Tools_Controller/tools_controller.py -in GCA_000005845.2_ASM584v2_genomic.fna -s 0 -amr 1
Traceback (most recent call last):
  File "/home/kevin/miniconda2/envs/superphy/bin/rgi", line 13, in <module>
    package.rgi.rgi.run()
  File "/home/kevin/miniconda2/envs/superphy/lib/python2.7/site-packages/package/rgi/rgi.py", line 984, in run
    main(args)
  File "/home/kevin/miniconda2/envs/superphy/lib/python2.7/site-packages/package/rgi/rgi.py", line 929, in main
    bpjson = runBlast(inType, inputSeq, threads, outputFile, criteria, data_type, clean, orf)
  File "/home/kevin/miniconda2/envs/superphy/lib/python2.7/site-packages/package/rgi/rgi.py", line 816, in runBlast
    with open(working_directory+"/"+outputFile+".json", 'w') as f:
IOError: [Errno 2] No such file or directory: '/home/kevin/dev/temp/Results/RGI/GCA_000005845.2_ASM584v2_genomic.json'
sh: 1: cannot create temp/Results/RGI/GCA_000005845.2_ASM584v2_genomic_FORMATTED.json: Directory nonexistent
cat: /home/kevin/dev/ecoli_serotyping-fork/src/RGI/../../temp/Results/RGI/GCA_000005845.2_ASM584v2_genomic.json: No such file or directory
Traceback (most recent call last):
  File "/home/kevin/dev/ecoli_serotyping-fork/src/Tools_Controller/../RGI/rgitool.py", line 166, in <module>
    getResults(genomesList, RGIpath)
  File "/home/kevin/dev/ecoli_serotyping-fork/src/Tools_Controller/../RGI/rgitool.py", line 81, in getResults
    with open(SCRIPT_DIRECTORY + '../../' + formatted_out + '.json', 'r') as temp_file:
IOError: [Errno 2] No such file or directory: '/home/kevin/dev/ecoli_serotyping-fork/src/RGI/../../temp/Results/RGI/GCA_000005845.2_ASM584v2_genomic_FORMATTED.json'
Traceback (most recent call last):
  File "ecoli_serotyping-fork/src/Tools_Controller/tools_controller.py", line 154, in <module>
    '-csv', str(args.csv), '-min', str(args.mingenomes), "-p", str(args.perfectMatches)])
  File "/home/kevin/miniconda2/envs/superphy/lib/python2.7/subprocess.py", line 219, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['/home/kevin/dev/ecoli_serotyping-fork/src/Tools_Controller/../RGI/rgitool.py', '--input', 'GCA_000005845.2_ASM584v2_genomic.fna', '-csv', '1', '-min', '1', '-p', '0']' returned non-zero exit status 1
kevin@kevin-HP-Z820-Workstation:~/dev|
⇒  ls
bigdata2.jnl
blazegraph.jar
blazegraph.jnl
card.tar
conf.properties
ecoli_serotyping
ecoli_serotyping2
ecoli_serotyping-fork
GCA_000005845.2_ASM584v2_genomic.fna
GCA_000005845.2_ASM584v2_genomic.fna.blastRes.xml
GCA_000005845.2_ASM584v2_genomic.fna.contig.fsa
GCA_000005845.2_ASM584v2_genomic.fna.contigToORF.fsa
GCA_000005845.2_ASM584v2_genomic.fna.predictedGenes.json
genomesSuperphy.ttl
genomes.ttl
get-pip.py
gfvo.xml
gm_key_64
go.owl
MetaGeneMark_linux_64
Miniconda2-latest-Linux-x86_64.sh
play3.rq
release-rgi-v3.1.1
rules.log
semantic
serotyping
sratoolkit.2.8.1-ubuntu64
superphy
superphy_conda
superphy-ectyper
superphy-testing
superphy-testing2
superphy-testing3
version-1
kevin@kevin-HP-Z820-Workstation:~/dev|
⇒  cat GCA_000005845.2_ASM584v2_genomic.fna.predictedGenes.json
{"U00096.3_1390": "ATGTCAGTACCCGTTCAACATCCTATGTATATCGATGGACAGTTTGTTACCTGGCGTGGAGACGCATGGATTGATGTGGTAAACCCTGCTACAGAGGCTGTCATTTCCCGCATACCCGATGGTCAGGCCGAGGATGCCCGTAAGGCAATCGATGCAGCAGAACGTGCACAACCAGAATGGGAAGCGTTGCCTGCTATTGAACGCGCCAGTTGGTTGCGCAAAATCTCCGCCGGGATCCGCGAACGCGCCAGTGAAATCAGTGCGCTGATTGTTGAAGAAGGGGGCAAGATCCAGCAGCTGGCTGAAGTCGAAGT