ERROR: failed to open file '5': No such file or directory

[robertwhbaldwin]

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]

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]

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]

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: nf-core/modules#5981
Bioconda PR: bioconda/bioconda-recipes#49282