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zerodel / sailfish-cir

a pipeline for quantification of circular RNA.
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sqlite3.OperationalError: unable to open database file #1

Open DadongZ opened 7 years ago

DadongZ commented 7 years ago

Hi There,

I got following issues when I was trying to run the program:

fasta=/data1/workspace/DCI/Kirsch/Jianguo.Huang/circRNA/bwaindex/genome.fa
gtf=/data1/Annotation/iGenome/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf
datdir=/data1/workspace/DCI/Kastan/Alternative_splicing/DRA005768/Data/fastq                                                                                                              outdir=/data1/workspace/DCI/Kirsch/Jianguo.Huang/circRNA/Results/japan                                                                                                                    
fastq1=${datdir}/DRR091835_1.fastq.gz                                                                                                                                                     
fastq2=${datdir}/DRR091835_2.fastq.gz 
PY=/opt/Anaconda3-4.4.0/bin/python3                                                                                                                                                       
 PG=/opt/NGS/sailfish-cir/sailfish-cir-0.11/sailfish_cir.py                                                                                                                                

 $PY $PG \                                                                                                                                                                                 
    -g $fasta \                                                                                                                                                                           
    -a $gtf \                                                                                                                                                                             
    -1 $fastq1 \                                                                                                                                                                          
    -2 $fastq2 \                                                                                                                                                                          
    --bed $output/DRR091835_ciri2.bed \                                                                                                                                                   
    --libtype ISR \                                                                                                                                                                       
    -o $output    
Traceback (most recent call last):
  File "/opt/NGS/sailfish-cir/sailfish-cir-0.11/sailfish_cir.py", line 1123, in <module>
    work_on_it.process_the_pipe_line()
  File "/opt/NGS/sailfish-cir/sailfish-cir-0.11/sailfish_cir.py", line 1004, in process_the_pipe_line
    self._cicular_pipeline()
  File "/opt/NGS/sailfish-cir/sailfish-cir-0.11/sailfish_cir.py", line 1058, in _cicular_pipeline
    do_make_gtf_for_circular_prediction(get_gff_database(self._annotation_file),
  File "/opt/NGS/sailfish-cir/sailfish-cir-0.11/sailfish_cir.py", line 706, in get_gff_database
    db = gffutils.create_db(gtf_file, db_file_path)
  File "/opt/Anaconda3-4.4.0/lib/python3.6/site-packages/gffutils/create.py", line 1286, in create_db
    c = cls(**kwargs)
  File "/opt/Anaconda3-4.4.0/lib/python3.6/site-packages/gffutils/create.py", line 696, in __init__
    super(_GTFDBCreator, self).__init__(*args, **kwargs)
  File "/opt/Anaconda3-4.4.0/lib/python3.6/site-packages/gffutils/create.py", line 107, in __init__
    conn = sqlite3.connect(dbfn)
sqlite3.OperationalError: unable to open database file

Any suggestions of the causes? Thanks

DadongZ commented 7 years ago

Just figured out. The error was due to the gtf directory is unwritable.