issue with scaffolding step

[Delaney-Nash]

Hi!

I'm having an issue running the script after installing with conda. This is the scaffold log file.

0:00:03.965568 Reading in original assembly 0:00:03.971603 Loading repeats Traceback (most recent call last): File "/home/d2nash/miniconda3/envs/gapless/bin/gapless.py", line 13327, in main(sys.argv[1:]) File "/home/d2nash/miniconda3/envs/gapless/bin/gapless.py", line 13156, in main GaplessScaffold(args[0], args[1], args[2], min_mapq, min_mapping_length, min_length_contig_break, prefix, stats) File "/home/d2nash/miniconda3/envs/gapless/bin/gapless.py", line 9066, in GaplessScaffold repeats = LoadRepeats(repeat_file, contig_ids) File "/home/d2nash/miniconda3/envs/gapless/bin/gapless.py", line 314, in LoadRepeats repeats['q_name'] = itemgetter(*repeats['q_name'])(contig_ids) TypeError: itemgetter expected 1 argument, got 0

And the other log files:

Split 3 scaffolds into 3 contigs and wrote it to: pass1/gapless_split.fa

[M::mm_idx_gen::0.0051.23] collected minimizers [M::mm_idx_gen::0.0074.32] sorted minimizers [M::main::0.0074.32] loaded/built the index for 3 target sequence(s) [M::mm_mapopt_update::0.0074.00] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 3 [M::mm_idx_stat::0.0083.87] distinct minimizers: 28801 (99.21% are singletons); average occurrences: 1.012; average spacing: 5.333; total length: 155420 [M::worker_pipeline::13.47013.78] mapped 64881 sequences [M::worker_pipeline::24.23714.27] mapped 65407 sequences [M::worker_pipeline::35.28114.45] mapped 65209 sequences [M::worker_pipeline::46.67614.56] mapped 63477 sequences [M::worker_pipeline::57.54314.65] mapped 61551 sequences [M::worker_pipeline::68.77414.67] mapped 58315 sequences [M::worker_pipeline::79.72914.69] mapped 57646 sequences [M::worker_pipeline::89.075*14.59] mapped 56711 sequences [M::main] Version: 2.26-r1175 [M::main] CMD: minimap2 -t 15 -x map-ont -c -N 5 --secondary=no pass1/gapless_split.fa /home/d2nash/Sequencing_Data/Nanopore/BQ1_Auguest_2023/delaney_bq1_aug4_23/no_sample/20220906_0428_MC-114136_FAT11060_b81d166d/Nanopore_Reads.fastq.gz [M::main] Real time: 89.182 sec; CPU: 1300.121 sec; Peak RSS: 5.087 GB

[M::mm_idx_gen::0.0031.61] collected minimizers [M::mm_idx_gen::0.0053.79] sorted minimizers [M::main::0.0053.79] loaded/built the index for 3 target sequence(s) [M::mm_mapopt_update::0.0053.52] mid_occ = 10 [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 3 [M::mm_idx_stat::0.0063.40] distinct minimizers: 15533 (99.55% are singletons); average occurrences: 1.007; average spacing: 9.934; total length: 155420 [M::worker_pipeline::0.0092.69] mapped 3 sequences [M::main] Version: 2.26-r1175 [M::main] CMD: minimap2 -t 15 -DP -k19 -w19 -m200 pass1/gapless_split.fa pass1/gapless_split.fa [M::main] Real time: 0.012 sec; CPU: 0.029 sec; Peak RSS: 0.005 GB

Thanks for your time!