Jeltje
commented
2 years ago It looks like Gallus_gallus.GRCg6a.102.gtf has annotations for chromosomes that are not present in Gallus_gallus.GRCg6a.dna_sm.toplevel.fa
Can you make sure that all chromosomes in the first field of the gtf are present with the exact same name in the fasta file?
For instance, if your annotation uses MT but the sequence is present as >chrMT or >mt you will get this error.
The same is true for flair.aligned.bed but I'm assuming you used Gallus_gallus.GRCg6a.dna_sm.toplevel.fa during flair align so that shouldn't be a problem.
Command: flair.py correct -q flair.aligned.bed -g ../00_ref/Gallus_gallus.GRCg6a.dna_sm.toplevel.fa -f ../00_ref/Gallus_gallus.GRCg6a.102.gtf
Step 1/5: Splitting junctions from GTF by chromosome: 100%|████████████████████████████████████| 39288/39288 [00:00<00:00, 57308.79it/s] Step 3/5: Preparing annotated junctions to use for correction: 100%|█████████████████████████████████| 160/160 [00:01<00:00, 140.47it/s] Step 4/5: Preparing reads for correction: 187929it [00:01, 183547.76it/s]███████████████████████████▌| 158/160 [00:01<00:00, 348.46it/s] Step 5/5: Correcting Splice Sites: 100%|████████████████████████████████████████████████████████████████| 50/50 [00:00<00:00, 50.59it/s] Traceback (most recent call last): 90%|█████████████████████████████████████████████████████████▌ | 45/50 [00:00<00:00, 50.73it/s] File "/group/zhougrp/dguan/nanopore_annotation/Chicken/24_flair/flair/bin/ssCorrect.py", line 425, in
main()
File "/group/zhougrp/dguan/nanopore_annotation/Chicken/24_flair/flair/bin/ssCorrect.py", line 407, in main
with open(os.path.join(tempDir, "%s_inconsistent.bed" % chrom),'rb') as fd:
FileNotFoundError: [Errno 2] No such file or directory: '/group/zhougrp/dguan/nanopore_annotation/Chicken/24_flair/tmp_c484aeea-2f06-4058-9a1a-de123aefec21/MT_inconsistent.bed'
Correction command did not exit with success status