Open zpliu1126 opened 4 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
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.
same issues as this #336
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?
What happened? test flair correct failed
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.
same issues as this #336