Open kmcoyle opened 1 month ago
Copy and paste the exact command you tried to run
flair align -g /projects/rmorin_scratch/ONT_scratch/results/ref/GRCh38_no_alt.fa -r 01-pychopper/fastq/10-40390T_full_length.fq.gz --output 02-bed12/10-40390T/ --threads 24
How did you install Flair?
bioconda (e.g. `conda create -n flair -c conda-forge -c bioconda flair`)
What happened?
[M::mm_idx_gen::97.927*1.91] collected minimizers [M::mm_idx_gen::114.286*4.15] sorted minimizers [M::main::114.287*4.15] loaded/built the index for 195 target sequence(s) [M::mm_mapopt_update::122.167*3.94] mid_occ = 751 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 195 [M::mm_idx_stat::124.997*3.88] distinct minimizers: 167240184 (35.46% are singletons); average occurrences: 6.007; average spacing: 3.086; total length: 3099922541 [M::worker_pipeline::239.875*11.87] mapped 932859 sequences [M::worker_pipeline::331.205*15.01] mapped 916887 sequences [M::worker_pipeline::423.103*16.86] mapped 910298 sequences [M::worker_pipeline::513.746*18.01] mapped 907468 sequences [M::worker_pipeline::613.348*18.89] mapped 905003 sequences [M::worker_pipeline::707.074*19.47] mapped 904138 sequences [M::worker_pipeline::795.307*19.91] mapped 901809 sequences [M::worker_pipeline::884.702*20.28] mapped 900953 sequences [M::worker_pipeline::970.547*20.56] mapped 898520 sequences [M::worker_pipeline::1058.106*20.81] mapped 896855 sequences [M::worker_pipeline::1140.977*21.02] mapped 897084 sequences [M::worker_pipeline::1221.754*21.09] mapped 879150 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -ax splice --secondary=no -t 24 /projects/rmorin_scratch/ONT_scratch/results/ref/GRCh38_no_alt.fa 01-pychopper/fastq/10-40390T_full_length.fq.gz [M::main] Real time: 1222.709 sec; CPU: 25761.669 sec; Peak RSS: 31.191 GB
What else do we need to know?
Output directory exists (02-bed12/10-40390T/) but there are no files in it. I have double checked the directory from which I ran the command, my home directory, the conda directory -- the files seem to have disappeared entirely.
Copy and paste the exact command you tried to run
How did you install Flair?
What happened?
What else do we need to know?
Output directory exists (02-bed12/10-40390T/) but there are no files in it. I have double checked the directory from which I ran the command, my home directory, the conda directory -- the files seem to have disappeared entirely.