BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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failed test for flair correct #352

Open zpliu1126 opened 2 months ago

zpliu1126 commented 2 months 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

How did you install Flair?

#* flair version 2.0
micromamba create -n flair -c conda-forge -c bioconda flair
micromamba activate flair

What happened? test flair correct failed

#? command I used 
cd  /path/to/falair/test/
make test-correct

mkdir -p test_output
mkdir -p test_diffs
flair correct -q test_input/test.align.bed -j test_input/shortread_junctions.tab -f test_input/annotation.incomplete.gtf -g test_input/genome.fa -o test_output/test.correct
Step 1/5: Splitting junctions from GTF by chromosome: 100%|█████████████████████████████████████████████████████████████████| 55/55 [00:00<00:00, 68738.59it/s]
Step 3/5: Preparing annotated junctions to use for correction: 100%|███████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 1020.84it/s]
Step 4/5: Preparing reads for correction: 1883it [00:00, 182457.94it/s]                                                                  | 0/3 [00:00<?, ?it/s]
Step 5/5: Correcting Splice Sites: 100%|█████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:01<00:00,  1.97it/s]
Traceback (most recent call last):  33%|█████████████████████████████▋                                                           | 1/3 [00:01<00:03,  1.52s/it]
  File "/public/home//micromamba/envs/flair/lib/python3.8/site-packages/flair/ssCorrect.py", line 423, in <module>
    main()
  File "/public/home/micromamba/envs/flair/lib/python3.8/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: 'test/0d3f9dac-fc63-40a8-9542-3b2e964ff8f4/chr12_inconsistent.bed'
Correction command did not exit with success status:
/public/home/micromamba/envs/flair/bin/python /public/home/micromamba/envs/flair/lib/python3.8/site-packages/flair/ssCorrect.py -i test_input/test.align.bed -w 15 -p 4 -o test_output/test.correct --progress -f test_input/genome.fa --correctStrand -j test_input/shortread_junctions.tab -g test_input/annotation.incomplete.gtf

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same issues as this #336