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dawelab / Ab10-Assembly

B73Ab10 genome assembly methods
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Some suggestions #2

Open EugeneKim76 opened 3 years ago

EugeneKim76 commented 3 years ago

Dear all,

I recently tested scripts in 4-Assembly folder and found what needs to be fixed.

  1. runpipeline.sh cp $core_genome ${output_dir}/core_assembly/step0_assembly/ . core_genome_file=${output_dir}/core_assembly/step0_assembly/$(basename ${core_genome}) cp $sup_genome ${output_dir}/sup_assembly/step0_assembly/ . sup_genome_file=${output_dir}/sup_assembly/step0_assembly/$(basename ${sup_genome}) cp $bionano_genome ${output_dir}/bionano_assembly/ . cp $bionano_errbin ${output_dir}/bionano_assembly/ . ->fixed cp $core_genome ${output_dir}/core_assembly/step0_assembly/ core_genome_file=${output_dir}/core_assembly/step0_assembly/$(basename ${core_genome}) cp $sup_genome ${output_dir}/sup_assembly/step0_assembly/ sup_genome_file=${output_dir}/sup_assembly/step0_assembly/$(basename ${sup_genome}) cp $bionano_genome ${output_dir}/bionano_assembly/ cp $bionano_errbin ${output_dir}/bionano_assembly/

  2. cut_conflicts.py cut_conflicts.py script produce errors when using fasta with headers including space. (ex. 1 000013F|arrow:1) Hence, I had to modify the headers of fasta using command lines below. cat genome.fasta | perl -ne 'chomp;if(/^>/){$ct++;print ">my_new_headername$ct\n";}else{print "$\n";}' > genome_header_modified.fasta

  3. step2-sv_fix.sh ngs_genome="$1" ->fixed genome="$1"

Best,

EugeneKim76 commented 3 years ago

Dear all,

I found additional errors. runpipeline.sh line 80 sh step4-hybrid_assembly.sh ${output_dir}/core_assembly/step3_merging/contig_overlap_merge/core_sup_merged_hybridassembly0.rmoverlap.fasta $bionano_genome $errbin ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0 -> fixed sh step4-hybrid_assembly.sh ${output_dir}/core_assembly/step3_merging/contig_overlap_merge/core_sup_merged_hybridassembly0.rmoverlap.fasta $bionano_genome $bionano_errbin ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0

runpipeline.sh line 92 sh step4-hybrid_assembly.sh ${output_dir}/core_assembly/step3_merging/contig_overlap_merge/core_sup_merged_hybridassembly0.rmoverlap.fasta $bionano_genome $errbin ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0 -> fixed sh step4-hybrid_assembly.sh ${output_dir}/core_assembly/step3_merging/contig_overlap_merge/core_sup_merged_hybridassembly0.rmoverlap.fasta $bionano_genome $bionano_errbin ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0

EugeneKim76 commented 3 years ago

Dear all, I found an additional error. The error is produced from final Overlap_merge.py of runpipeline.sh and solved by correction as shown below

line 83-86 of runpipeline.sh python Overlap_merge.py \ -x ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0/_NGScontigs_HYBRID_SCAFFOLD.xmap \ -k ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0/_key.txt.cut.txt \ -o ${output_dir}/core_assembly/step4_hybridassembly/overlap_mer

->fixed cp ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0/hybrid_scaffolds/core_sup_merged_hybridassembly0.rmoverlap.fasta.cut.fasta ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0/hybrid_scaffolds/core_sup_merged_hybridassembly0.rmoverlap.fasta python Overlap_merge.py \ -x ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0/_NGScontigs_HYBRID_SCAFFOLD.xmap \ -k ${output_dir}/core_assembly/step4_hybridassembly/hybridassembly0/_key.txt.cut.txt \ -o ${output_dir}/core_assembly/step4_hybridassembly/overlap_mer