Hello. I’m trying to use the FLAIRcorrect tool to correct splice site calls in a cDNA alignments from a nanopore dataset. The tool is returning 0 lines of data. The job information shows the following:
Tool standard output: [E::fai_build3_core] Failed to open the file reference.fa
[faidx] Could not build fai index reference.fa.fai
Tool standard error: Error running samtools faidx for indexing fasta reference for flair
index file reference.fa.fai not found, generating…
WARNING. chromosome (chrX) was not found in the FASTA file. Skipping.
Step 1/5: Splitting junctions from GTF by chromosome: 0%| | 0/13 [00:00<?, ?it/s]e[A
Step 1/5: Splitting junctions from GTF by chromosome: 100%|██████████| 13/13 [00:00<00:00, 49122.48it/s]
Step 3/5: Preparing annotated junctions to use for correction: 0%| | 0/1 [00:00<?, ?it/s]e[A
Step 3/5: Preparing annotated junctions to use for correction: 100%|██████████| 1/1 [00:00<00:00, 203.40it/s]
Step 4/5: Preparing reads for correction: 0it [00:00, ?it/s]e[A
Step 4/5: Preparing reads for correction: 38571it [00:00, 384514.92it/s]e[A
Step 4/5: Preparing reads for correction: 39522it [00:00, 387437.99it/s]
Step 5/5: Correcting Splice Sites: 0it [00:00, ?it/s]e[A
Step 5/5: Correcting Splice Sites: 0it [00:00, ?it/s]
Can someone interpret the output and error to tell me if the tool is running correctly? I get a similar output whether I use a reference fasta file from the single gene I’m analyzing, or using the locally cached hg38 assembly.
Could the 0 line output result from insufficient number of input alignments? My bed12 file has 39,000 regions.
Thanks in advanced for any insight.
