BESST: error: argument -orientation is required

[Inexperiencedresearcher]

Hello!

I am trying to use GATB-minia-pipeline to assemble a genome. Because my storage is limited, I am not doing a multi-k but instead a k=41.

the assembly with minia works without issues, however when performing a scaffold with BESST I ran into the following issue:

(2021-08-10 11:41:36) Finished Multi-k GATB-Pipeline at k=41

(2021-08-10 11:41:38) Execution of 'python BESST/scripts/reads_to_ctg_map.py'. Command line:
python /home/sp1615/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py --tmp_path /home/sp1615/Desktop/T51_genome_assembly/BESST_tmp --threads 40 T51_S8_R1_001.fastq.gz T51_S8_R2_001.fastq.gz assembly_k41.contigs.fa assembly.lib_0

pe1_path: T51_S8_R1_001.fastq.gz
pe2_path: T51_S8_R2_001.fastq.gz
genome_path: assembly_k41.contigs.fa
output_path: assembly.lib_0
tmp_path: /home/sp1615/Desktop/T51_genome_assembly/BESST_tmp
bwa path: bwa
number of threads: 40
Remove temp SAM and BAM files: No
Use bwa aln and sampe instead of bwa mem: No
Do not rebuild bwa index if already exists in tmp dir: No

Start processing.

Aligning with bwa mem.
Temp directory: /home/sp1615/Desktop/T51_genome_assembly/BESST_tmp
Output path: assembly.lib_0
Stderr file: assembly.lib_0.bwa.1
Make bwa index... Done.
Align with bwa mem... Done.
Time elapsed for bwa index and mem: 5:43:13.571824

Convert SAM to BAM... Done.
Time elapsed for SAM to BAM conversion: 2:09:30.058622

Sort BAM... Done.
Time elapsed for BAM sorting: 4:17:52.790747

Index BAM... Done.
Time elapsed for BAM indexing: 0:14:52.160132

Remove temp files... Done.
Time elapsed for temp files removing: 0:00:16.807376

Processing is finished.
(2021-08-11 00:07:30) Execution of 'python BESST/runBESST'. Command line:
/home/sp1615/gatb-minia-pipeline/tools/memused python /home/sp1615/gatb-minia-pipeline/BESST/runBESST -c assembly_k41.contigs.fa -f assembly.lib_0.bam -o assembly_besst --orientation fr --iter 10000
usage: BESST [-h] -c CONTIGFILE -f BAMFILES [BAMFILES ...] -orientation
ORIENTATION [ORIENTATION ...] [-r READLEN [READLEN ...]]
[-m MEAN [MEAN ...]] [-s STDDEV [STDDEV ...]] [-z COVCUTOFF]
[-z_min LOWER_COVCUTOFF] [-T THRESHOLD [THRESHOLD ...]]
[-e EDGESUPPORT [EDGESUPPORT ...]] [-k MINSIZE [MINSIZE ...]]
[-filter_contigs CONTIG_FILTER_LENGTH] [--min_mapq MIN_MAPQ]
[--iter PATH_THRESHOLD] [--score_cutoff SCORE_CUTOFF]
[--max_extensions MAX_EXTENSIONS] [-a HAPLRATIO]
[-b HAPLTHRESHOLD] [-K KMER] [-M MMER] [-g] [-o OUTPUT] [-d] [-y]
[-q] [--no_score] [-devel] [-plots] [--separate_repeats]
[--NO_ILP] [--FASTER_ILP] [--print_scores] [--dfs_traversal]
[--bfs_traversal] [-max_contig_overlap MAX_CONTIG_OVERLAP]
[--version]
BESST: error: argument -orientation is required
maximal memory used: 6 MB
(2021-08-11 00:07:31) Execution of 'python BESST/runBESST' failed. Command line:
/home/sp1615/gatb-minia-pipeline/tools/memused python /home/sp1615/gatb-minia-pipeline/BESST/runBESST -c assembly_k41.contigs.fa -f assembly.lib_0.bam -o assembly_besst --orientation fr --iter 10000

I noticed here #25 that there seems to be an issue with how the gatb script calls BESST which can be fixed by changing line 469 from -orientation to --orientation.

however, this is the gatb script version I have at line 469:

cmd = ['-c', contigs, '-f'] + bam_files + ['-o', prefix + '_besst'] + ['--orientation'] + orientations + ['--iter', besst_iter]

which already has the change from -orientation to --orientation.

should I change it back to -orientation?

thank you for your help!
S

[rchikhi]

hi, yes please try this change, but also if you have only paired-end reads, you could also just skip scaffolding or pre-merge pairs if they're overlapping. Assembly result shouldn't be drastically different.

[rchikhi]

your assembly is already in the file assembly_k41.contigs.fa and you can consider it to be the final result of the pipeline (without scaffolding)

[Inexperiencedresearcher]

Thank you for your reply, I have tried changing it to -orientation and it works.

also, I tried multi-k assembly + scaffolding (I managed to increase my storage) and it all works, but I have yet to check whether the scaffolding with BESST has improved the asssemblies at various k values.