BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
Other
201 stars 69 forks source link

flair correct shows FileNotFoundError #336

Open guo0814 opened 1 month ago

guo0814 commented 1 month ago

Copy and paste the exact command you tried to run Feel free to leave any original paths, we don't have access to your system flair correct -q /home/dragon/Database/Guoyingyu/1_flair.aligned.bed -f /home/dragon/Database/Guoyingyu/Homo_sapiens.GRCh38.111.gtf -g /home/dragon/Database/Guoyingyu/Homo_sapiens.GRCh38.dna.toplevel.fa How did you install Flair?1. bioconda (We'd prefer it if you used one of the top two because they are the least likely to have package compatibility problems.)

  1. bioconda (e.g. conda create -n flair -c conda-forge -c bioconda flair)
  2. docker pull brookslab/flair:latest
  3. pip
  4. downloaded latest release from github
  5. git cloned the current repository
  6. conda env create -f misc/flair_basic_conda_env.yaml

What happened?

File "/home/dragon/Database/Guoyingyu/.local/lib/python3.6/site-packages/flair/ssCorrect.py", line 423, in <module>
    main()
  File "/home/dragon/Database/Guoyingyu/.local/lib/python3.6/site-packages/flair/ssCorrect.py", line 402, in main
    with open(os.path.join(tempDir, "%s_inconsistent.bed" % chrom),'rb') as fd:
FileNotFoundError: [Errno 2] No such file or directory: '/home/dragon/Database/Guoyingyu/ef3ebff9-6175-4b23-8bdf-e85042d809b8/1_inconsistent.bed'
Correction command did not exit with success status:
/usr/bin/python3 /home/dragon/Database/Guoyingyu/.local/lib/python3.6/site-packages/flair/ssCorrect.py -i /home/dragon/Database/Guoyingyu/2_flair.aligned.bed -w 15 -p 4 -o flair --progress -f /home/dragon/Database/Guoyingyu/Homo_sapiens.GRCh38.dna.toplevel.fa -g /home/dragon/Database/Guoyingyu/Homo_sapiens.GRCh38.111.gtf --print_check

We know it's ugly but we promise it helps us solve problems faster.

What else do we need to know? Go ahead, every bit helps.