temporary files to /tmp/tmpb1of3jhx/
Making transcript fasta using annotated gtf and genome sequence
Aligning reads to reference transcripts
Minimap2 issue, check stderr file
What else do we need to know?
stderr file:
[M::mm_idx_gen::108.0671.58] collected minimizers
[M::mm_idx_gen::139.5541.50] sorted minimizers
[M::main::140.7221.49] loaded/built the index for 254129 target sequence(s)
[M::mm_mapopt_update::147.6341.46] mid_occ = 125
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 254129
[M::mm_idx_stat::147.877*1.46] distinct minimizers: 20889310 (42.03% are singletons); average occurrences: 3.938; average spacing: 5.397; total length: 443903693
flair collapse -g /home/lucilaviappiani/genoma/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --gtf /home/lucilaviappiani/genoma/gtf/Homo_sapiens.GRCh38.112.gtf -q /home/lucilaviappiani/flair/barcode14_8/flair_all_corrected.bed -r /home/lucilaviappiani/8.7.24/merge148_filtradas.fastq --stringent --check_splice --generate_map --annotation_reliant generate
How did you install Flair?
conda create -n flair -c conda-forge -c bioconda flair)What happened?
temporary files to /tmp/tmpb1of3jhx/ Making transcript fasta using annotated gtf and genome sequence Aligning reads to reference transcripts Minimap2 issue, check stderr file
What else do we need to know?
stderr file: [M::mm_idx_gen::108.0671.58] collected minimizers [M::mm_idx_gen::139.5541.50] sorted minimizers [M::main::140.7221.49] loaded/built the index for 254129 target sequence(s) [M::mm_mapopt_update::147.6341.46] mid_occ = 125 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 254129 [M::mm_idx_stat::147.877*1.46] distinct minimizers: 20889310 (42.03% are singletons); average occurrences: 3.938; average spacing: 5.397; total length: 443903693