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agshumate / Liftoff

An accurate GFF3/GTF lift over pipeline
GNU General Public License v3.0
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ERROR: failed to open file '5': No such file or directory #128

Open robertwhbaldwin opened 2 years ago

robertwhbaldwin commented 2 years ago

Here's the command I used:

liftoff \ -g GCF_910596095.1_fThuMac1.1_genomic.gff \ -o ./lift.gff \ -dir ./intermediate_files \ -a 0.7 \ -s 0.7 \ -flank 0.1 \ -exclude_partial \ -copies \ -cds \ -mm2_options="-r 2k -z 5000" \ T_orientalis_final.fasta \ GCF_910596095.1_fThuMac1.1_genomic.fna \

Here's the log file:

./liftoff.sh extracting features 2022-08-25 18:11:35,367 - INFO - Populating features 2022-08-25 18:13:04,889 - INFO - Populating features table and first-order relations: 1426522 features 2022-08-25 18:13:04,890 - INFO - Updating relations 2022-08-25 18:13:17,262 - INFO - Creating relations(parent) index 2022-08-25 18:13:17,976 - INFO - Creating relations(child) index 2022-08-25 18:13:18,882 - INFO - Creating features(featuretype) index 2022-08-25 18:13:19,415 - INFO - Creating features (seqid, start, end) index 2022-08-25 18:13:20,072 - INFO - Creating features (seqid, start, end, strand) index 2022-08-25 18:13:20,779 - INFO - Running ANALYZE features aligning features [M::main::2.6651.02] loaded/built the index for 101 target sequence(s) [M::mm_mapopt_update::3.5111.01] mid_occ = 195 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 101 [M::mm_idx_stat::4.1481.01] distinct minimizers: 59155405 (56.81% are singletons); average occurrences: 2.559; average spacing: 5.314; total length: 804502418 [M::worker_pipeline::886.4411.00] mapped 24998 sequences [M::worker_pipeline::1238.045*1.00] mapped 8320 sequences ERROR: failed to open file '5': No such file or directory ERROR: failed to map the query file

Something tells me the mm2_options is the problem but I used exactly what was posted in the documentation on this github page. It doesn't look right compared to what is stated in minimap2 doc regarding the -r and -z options.

agshumate commented 2 years ago

hi, this is an issue with mm2_options but I believe it still should have run to completion? Did the expected output file get generated?

mlplace commented 1 year ago

It appears all that needs to be done is add a space after the first quote mark and the error goes away : args.mm2_options += "--end-bonus 5" becomes args.mm2_options += " --end-bonus 5"

GallVp commented 1 month ago

I am also getting,

ERROR: failed to open file '5'

See GitHub CI run with error: https://github.com/nf-core/modules/actions/runs/9951732936/job/27491785371

It seems to be fixed when using minimap2 version 2.24: https://github.com/nf-core/modules/actions/runs/9951336845/job/27490669473

nf-core modules PR: https://github.com/nf-core/modules/pull/5981 Bioconda PR: https://github.com/bioconda/bioconda-recipes/pull/49282