chromosome_scaffolder.sh: error: " Could not parse delta file"

Hi everyone I am new to MaSuRCA Reference guided assembly. I am using chromosome_scaffolder.sh for scaffoding. I have shared the log info, I don't know what is the error. Could you help me with this?

Log info:

shift
[[ 0 > 0 ]] ++ basename GCA_028751855.1_ASM2875185v1_genomic.fna
REF_CHR=GCA_028751855.1_ASM2875185v1_genomic.fna ++ basename ./primary.genome.scf.fasta
HYB_CTG=primary.genome.scf.fasta.split
HYB_POS=primary.genome.scf.fasta.split.posmap
PREFIX=GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.gaps.success ']'
log 'Computing gap coordinates in the reference' ++ date
dddd='Thu Aug 22 10:35:43 AM IST 2024'
echo -e '[Thu Aug 22 10:35:43 AM IST 2024] Computing gap coordinates in the reference' [Thu Aug 22 10:35:43 AM IST 2024] Computing gap coordinates in the reference
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.scaffold.success
MaSuRCA-4.0.9/bin/splitFileAtNs GCA_028751855.1_ASM2875185v1_genomic.fna 1
perl -ane '{$h{substr($F[1],3)}=$F[0]}END{while($line=){chomp($line);@f=split(/\s+/,$line);print "$f[0] $h{$f[1]} ",$f[2]+1," $f[3] $f[4]\n";}}' scaffNameTranslations.txt
awk 'BEGIN{pg=0}{print $2" "pg" "$3;pg=$4}'
mv GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.gap_coordinates.txt.tmp GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.gap_coordinates.txt
rm scaffNameTranslations.txt genome.asm genome.posmap.ctgscf
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.gaps.success
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.split.success ']'
log 'Splitting query scaffolds at >100bp gaps' ++ date
dddd='Thu Aug 22 10:36:19 AM IST 2024'
echo -e '[Thu Aug 22 10:36:19 AM IST 2024] Splitting query scaffolds at >100bp gaps' [Thu Aug 22 10:36:19 AM IST 2024] Splitting query scaffolds at >100bp gaps
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.readalign.success
MaSuRCA-4.0.9/bin/splitScaffoldsAtNs.sh ./primary.genome.scf.fasta 100
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.split.success
'[' 1 -gt 0 ']'
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.noise.success ']'
log 'Adding noise to reference to align to duplicated regions' ++ date
dddd='Thu Aug 22 10:36:26 AM IST 2024'
echo -e '[Thu Aug 22 10:36:26 AM IST 2024] Adding noise to reference to align to duplicated regions' [Thu Aug 22 10:36:26 AM IST 2024] Adding noise to reference to align to duplicated regions
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.align1.success
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.align2.success
MaSuRCA-4.0.9/bin/introduce_errors_fasta_file.pl GCA_028751855.1_ASM2875185v1_genomic.fna 0.002 1
MaSuRCA-4.0.9/bin/fix_consensus_from_vcf.pl GCA_028751855.1_ASM2875185v1_genomic.fna
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.noise.success
'[' 0 -lt 1 ']'
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.readalign.success ']'
log 'Mapping reads to query contigs' ++ date
dddd='Thu Aug 22 10:42:08 AM IST 2024'
echo -e '[Thu Aug 22 10:42:08 AM IST 2024] Mapping reads to query contigs' [Thu Aug 22 10:42:08 AM IST 2024] Mapping reads to query contigs
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.coverage.success
[[ ./superReadSequences.fasta = *.fa ]]
[[ ./superReadSequences.fasta = *.fasta ]]
MaSuRCA-4.0.9/bin/../Flye/bin/flye-minimap2 -x map-pb -t 10 -N 1 -a primary.genome.scf.fasta.split ./superReadSequences.fasta
gzip -c -1
mv GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.sam.gz.tmp GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.sam.gz
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.readalign.success
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.coverage.success ']'
log 'Computing read coverage of query contigs' ++ date
dddd='Thu Aug 22 10:48:21 AM IST 2024'
echo -e '[Thu Aug 22 10:48:21 AM IST 2024] Computing read coverage of query contigs' [Thu Aug 22 10:48:21 AM IST 2024] Computing read coverage of query contigs
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.break.success
awk '{if($0 ~ /^@/) print $0; else if($5>=20) print $0}'
cat /dev/fd/63 /dev/fd/62
MaSuRCA-4.0.9/bin/samToDelta
MaSuRCA-4.0.9/bin/show-coords -lcH /dev/stdin ++ gunzip -c GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.sam.gz
awk '{print $NF" "$(NF-1)" "$1"\n"$NF" "$(NF-1)" "$2}' ++ ufasta sizes -H primary.genome.scf.fasta.split
sort -k2,2 -k3,3n -S 20%
MaSuRCA-4.0.9/bin/compute_coverage.pl ++ awk '{print "@SQ\tSN:"$1"\tLN:"$2}'
mv primary.genome.scf.fasta.split.posmap.coverage.tmp primary.genome.scf.fasta.split.posmap.coverage
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.coverage.success
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.align1.success ']'
log 'Aligning query contigs to reference scaffolds' ++ date
dddd='Thu Aug 22 10:50:39 AM IST 2024'
echo -e '[Thu Aug 22 10:50:39 AM IST 2024] Aligning query contigs to reference scaffolds' [Thu Aug 22 10:50:39 AM IST 2024] Aligning query contigs to reference scaffolds
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.filter1.success
MaSuRCA-4.0.9/bin/nucmer -t 10 -p GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split -c 200 GCA_028751855.1_ASM2875185v1_genomic.fna.w_noise primary.genome.scf.fasta.split
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.align1.success
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.filter1.success ']'
log 'Filtering the alignments' ++ date
dddd='Thu Aug 22 11:03:59 AM IST 2024'
echo -e '[Thu Aug 22 11:03:59 AM IST 2024] Filtering the alignments' [Thu Aug 22 11:03:59 AM IST 2024] Filtering the alignments
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.merge1.success
MaSuRCA-4.0.9/bin/delta-filter -1 -i 97 GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.delta
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.filter1.success
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.merge1.success ']'
log 'Merging alignments' ++ date
dddd='Thu Aug 22 11:03:59 AM IST 2024'
echo -e '[Thu Aug 22 11:03:59 AM IST 2024] Merging alignments' [Thu Aug 22 11:03:59 AM IST 2024] Merging alignments
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.break.success
show-coords -lcHr GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.1.delta
MaSuRCA-4.0.9/bin/merge_matches_and_tile_coords_file.pl 100000
awk 'BEGIN{last_end=0;last_scf="";}{if($18 != last_scf){last_end=$2;last_scf=$18} if($2>last_end-10000) {print $0; last_end=$2}}'
awk '{if($16>5 || $7>5000 ) print $0}'
cat GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.1.coords
perl -ane '{$chrom{$F[-1]}.="$F[-2] "}END{foreach $c(keys %chrom){my %temp=();@f=split(/\s+/,$chrom{$c});foreach $t(@f){$temp{$t}=1}print "$c ",scalar(keys %temp),"\n";}}'
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.merge1.success
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.break.success ']'
log 'Splitting query contigs at suspect locations' ++ date
dddd='Thu Aug 22 11:03:59 AM IST 2024'
echo -e '[Thu Aug 22 11:03:59 AM IST 2024] Splitting query contigs at suspect locations' [Thu Aug 22 11:03:59 AM IST 2024] Splitting query contigs at suspect locations
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.align2.success ++ awk '{print $4}' primary.genome.scf.fasta.split.posmap.coverage ++ sort -n -S 10% ++ uniq -c ++ sort -nrk1,1 -S 10% ++ head -n 1 ++ awk '{print int($2/.8)}'
let AUTO_REP_COV_THRESH=3
'[' 3 -lt 2 ']'
'[' -1 -lt 0 ']'
let REP_COV_THRESH=3
'[' -1 -lt 0 ']'
let COV_THRESH=1
log 'Using low coverage threshold 1 and repeat coverage threshold 3' ++ date
dddd='Thu Aug 22 11:04:09 AM IST 2024'
echo -e '[Thu Aug 22 11:04:09 AM IST 2024] Using low coverage threshold 1 and repeat coverage threshold 3' [Thu Aug 22 11:04:09 AM IST 2024] Using low coverage threshold 1 and repeat coverage threshold 3
awk '{if($4<$5) print $4" "$5" "($4+$5)/2" "$NF" "$13; else print $5" "$4" "($4+$5)/2" "$NF" "$13;}' GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.1.coords
perl -e '{open(FILE,"GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.contig_chromosome_count.txt");while($line=){chomp($line);($ctg,$cnt)=split(/\s+/,$line);$count{$ctg}=$cnt;} while($line=){chomp($line);@t=split(/\s+/,$line);print "$line\n" if($count{$t[-2]}>1);}}'
sort -k4,4 -k1,1n -S 10%
uniq -D -f 3
awk '{if($NF != prev){offset=$2;prev=$NF;print $0}else if($2>offset){print $0;offset=$2;}}'
uniq -D -f 3
awk '{if($4==ctg){if($1>5000 && $1<$NF-5000) print "alnbreak "$4" "$1" 0"}else{ctg=$4;if($2>5000 && $2<$NF-5000) print "alnbreak "$4" "$2" 0"}}'
cat GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.1.coords.breaks primary.genome.scf.fasta.split.posmap.coverage
sort -k2,2 -k3,3n -S 10%
grep -C 50 break primary.genome.scf.fasta.split.posmap.coverage.w_breaks
sort -k2,2 -k3,3n -S 10%
MaSuRCA-4.0.9/bin/evaluate_splits.pl /dev/fd/63 ++ ufasta sizes -H primary.genome.scf.fasta.split ++ awk '{print $1" "$2}'
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.align2.success ']'
log 'Aligning contigs to the reference pass2' ++ date
dddd='Thu Aug 22 11:04:27 AM IST 2024'
echo -e '[Thu Aug 22 11:04:27 AM IST 2024] Aligning contigs to the reference pass2' [Thu Aug 22 11:04:27 AM IST 2024] Aligning contigs to the reference pass2
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.filter2.success
MaSuRCA-4.0.9/bin/nucmer -t 10 -p GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.broken -c 200 GCA_028751855.1_ASM2875185v1_genomic.fna.w_noise primary.genome.scf.fasta.split.broken terminate called after throwing an instance of 'std::runtime_error' what(): Can't open file 'primary.genome.scf.fasta.split.broken' MaSuRCA-4.0.9/bin/chromosome_scaffolder.sh: line 248: 8859 Aborted (core dumped) $MYPATH/nucmer -t $NUM_THREADS -p $REF_CHR.$HYB_CTG.broken -c 200 $REF_CHR.w_noise $HYB_CTG.broken
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.filter2.success ']'
log 'Filtering the alignments' ++ date
dddd='Thu Aug 22 11:14:07 AM IST 2024'
echo -e '[Thu Aug 22 11:14:07 AM IST 2024] Filtering the alignments' [Thu Aug 22 11:14:07 AM IST 2024] Filtering the alignments
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.scaffold.success
MaSuRCA-4.0.9/bin/delta-filter -r -i 97 GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.broken.delta
MaSuRCA-4.0.9/bin/delta-filter -q /dev/stdin ERROR: Could not parse delta file, GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.broken.delta error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402
'[' '!' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.scaffold.success ']'
rm -f GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.place_extra.success
log 'Final scaffolding' ++ date
dddd='Thu Aug 22 11:14:07 AM IST 2024'
echo -e '[Thu Aug 22 11:14:07 AM IST 2024] Final scaffolding' [Thu Aug 22 11:14:07 AM IST 2024] Final scaffolding
touch GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.fillseq.fa
MaSuRCA-4.0.9/bin/show-coords -lcHr -I 97 GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.broken.1.delta
MaSuRCA-4.0.9/bin/merge_matches_and_tile_coords_file.pl 100000
awk '{if($15>25 || $16>25 || $8>25000) print $0}'
awk 'BEGIN{last_end=0;last_scf="";}{if($18 != last_scf){last_end=$2;last_scf=$18} if($2>=last_end) {print $0; last_end=$2}}'
MaSuRCA-4.0.9/bin/extract_single_best_match_coords_file.pl ERROR: Could not parse delta file, GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.broken.1.delta error no: 402
awk '{if($4<$5){print $1-$4+1" "$1-$4+$13+1" "$0}else{print $1-($13-$4)" "$1+$4" "$0}}'
sort -k20,20 -k1,1n -S 10%
awk 'BEGIN{ch="";cend=0;}{if(ch == $20){if($2-cend > -1*int("200")){print $3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17,$18,$19,$20,$21;cend=$2}}else{print $3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17,$18,$19,$20,$21;;cend=$2;ch=$20;}}'
cat GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.reconciled.txt
MaSuRCA-4.0.9/bin/output_reconciled_scaffolds.pl /dev/fd/63 ++ cat GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.fillseq.fa primary.genome.scf.fasta.split.broken cat: GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.reconciled.txt: No such file or directory cat: primary.genome.scf.fasta.split.broken: No such file or directory
'[' -e GCA_028751855.1_ASM2875185v1_genomic.fna.primary.genome.scf.fasta.split.scaffold.success ']'

alekseyzimin / masurca

chromosome_scaffolder.sh: error: " Could not parse delta file" #347