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bcgsc / LongStitch

Correct and scaffold assemblies using long reads
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[ERRORS] A helper process has finished unsuccessfully and Process pipeline: Spawner process failed. #78

Closed francicco closed 6 months ago

francicco commented 8 months ago

Hi,

I'm trying to use longstich with ont data on an assebly done with flye. But I'm betting this errors. I don't quite understand the nature of the errors.

Thanks a lot F

longstitch tigmint-ntLink-arks draft=DraftGenome reads=ont_reads G=250000000 w=150 k_ntLink=24 longmap=ont
tigmint-make tigmint-long draft=DraftGenome reads=ont_reads cut=250 t=8 G=250000000 span=auto dist=auto
make[1]: Entering directory '/user/work/tk19812/HoneyPotProject/ONTREADS/Mbag.0.7.FlyeGenome'
/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/tigmint_estimate_dist.py ont_reads.fasta -n 1000000 -o ont_reads.tigmint-long.params.tsv
sh -c '/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/../src/long-to-linked-pe -l 250 -m2000 -g250000000 -s -b ont_reads.barcode-multiplicity.tsv --bx -t8 --fasta -f ont_reads.tigmint-long.params.tsv ont_reads.fasta | \
minimap2 -y -t8 -x map-ont --secondary=no DraftGenome.fa - | \
/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/tigmint_molecule_paf.py -q0 -s2000 -p ont_reads.tigmint-long.params.tsv - | sort -k1,1 -k2,2n -k3,3n  > DraftGenome.ont_reads.cut250.molecule.size2000.distauto.bed'
long-to-linked-pe v1.2.9: Using more than 6 threads does not scale, reverting to 6.
[M::mm_idx_gen::6.158*1.51] collected minimizers
[M::mm_idx_gen::6.837*2.10] sorted minimizers
[M::main::6.837*2.10] loaded/built the index for 4722 target sequence(s)
[M::mm_mapopt_update::7.172*2.05] mid_occ = 186
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 4722
[M::mm_idx_stat::7.407*2.01] distinct minimizers: 24327762 (74.78% are singletons); average occurrences: 1.959; average spacing: 5.243; total length: 249827693
[M::worker_pipeline::19.707*4.58] mapped 631548 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -y -t8 -x map-ont --secondary=no DraftGenome.fa -
[M::main] Real time: 19.827 sec; CPU: 90.306 sec; Peak RSS: 2.083 GB
samtools faidx DraftGenome.fa
/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/tigmint-cut -p8 -w1000 -t0 -m3000 -f ont_reads.tigmint-long.params.tsv -o DraftGenome.ont_reads.cut250.molecule.size2000.distauto.trim0.window1000.spanauto.breaktigs.fa DraftGenome.fa DraftGenome.ont_reads.cut250.molecule.size2000.distauto.bed
Started at: 2024-02-24 11:54:30.008043
Reading contig lengths...
Finding breakpoints...
Attempted corrections: 0
Cutting assembly at breakpoints...
DONE!
Ended at: 2024-02-24 11:54:32.934475
ln -sf DraftGenome.ont_reads.cut250.molecule.size2000.distauto.trim0.window1000.spanauto.breaktigs.fa DraftGenome.cut250.tigmint.fa
make[1]: Leaving directory '/user/work/tk19812/HoneyPotProject/ONTREADS/Mbag.0.7.FlyeGenome'
ntLink  scaffold target=DraftGenome.cut250.tigmint.fa reads="ont_reads.fasta.gz" t=8 k=24 w=150 z=1000 n=2 a=1 conservative=True
make[1]: Entering directory `/user/work/tk19812/HoneyPotProject/ONTREADS/Mbag.0.7.FlyeGenome'
indexlr --long --pos --strand -k 24 -w 150 -t 8 DraftGenome.cut250.tigmint.fa > DraftGenome.cut250.tigmint.fa.k24.w150.tsv
indexlr 1.4.9: Using more than 5 threads does not scale, reverting to 5.
sh -c 'pigz -p8 -f -cd ont_reads.fasta.gz | \
indexlr --long --pos --strand --len -k 24 -w 150 -t 8 - | \
/user/work/tk19812/software/ntLink-1.3.8/bin/ntlink_pair.py -p DraftGenome.cut250.tigmint.fa.k24.w150.z1000 -n 2 -m DraftGenome.cut250.tigmint.fa.k24.w150.tsv -s DraftGenome.cut250.tigmint.fa  \
-k 24 -a 1 -z 1000 -f 10 -x 0  --verbose -'
indexlr 1.4.9: Using more than 5 threads does not scale, reverting to 5.
Running pairing stage of ntLink ...

Parameters:
    Read minimizer files:  ['-']
    -s  DraftGenome.cut250.tigmint.fa
    -m  DraftGenome.cut250.tigmint.fa.k24.w150.tsv
    -p  DraftGenome.cut250.tigmint.fa.k24.w150.z1000
    -n  2
    -k  24
    -a  1
    -z  1000
    -f  10
    -x  0.0
2024-02-24 11:54:54.940797 : Reading minimizers DraftGenome.cut250.tigmint.fa
2024-02-24 11:55:04.067036 : Reading fasta file DraftGenome.cut250.tigmint.fa
2024-02-24 11:55:04.619099 : Finding pairs
2024-02-24 11:55:16.863542 : Building scaffold graph
2024-02-24 11:55:16.865123 : Filtering the graph
2024-02-24 11:55:16.867185 : Printing graph DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot
2024-02-24 11:55:16.874473 : DONE!
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 2 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 3 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n3.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n3.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 4 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n4.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n4.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 5 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n5.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n5.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 6 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n6.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n6.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 7 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n7.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n7.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 8 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n8.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n8.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 9 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n9.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n9.abyss-scaffold.path.sterr'
sh -c 'cat DraftGenome.cut250.tigmint.fa | \
cut -d " " -f1  | \
abyss-scaffold -k2 -n 10 -s1000 --min-gap 20 - DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot 1> DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n10.abyss-scaffold.path 2>DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n10.abyss-scaffold.path.sterr'
/user/work/tk19812/software/ntLink-1.3.8/bin/ntlink_stitch_paths.py --min_n 2 --max_n 10  -p out \
-g DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot --conservative DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n3.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n4.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n5.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n6.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n7.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n8.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n9.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n10.abyss-scaffold.path -o DraftGenome.cut250.tigmint.fa.k24.w150.z1000.stitch.path
Running ntLink stitch paths stage...

2024-02-24 11:56:17.545336  : Finding optimal n...
2024-02-24 11:56:17.547232  : Optimal n = 2 at N50 = 6759937.0
2024-02-24 11:56:17.547271 : Building path graph
2024-02-24 11:56:17.548225 : Reading scaffold file DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot
Printing paths for optimal N50, no stitching...

2024-02-24 11:56:17.550356 : Finding paths

Total number of components in graph: 34 

rm -f DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n*.abyss-scaffold.path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n*.abyss-scaffold.path.sterr
sh -c '/user/work/tk19812/software/ntLink-1.3.8/bin/ntlink_filter_sequences.py --fasta DraftGenome.cut250.tigmint.fa \
--dot DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot --path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.stitch.path -k 15 -g 20 -t 8 |\
indexlr --long --pos -k 15 -w 5 -t 8 - |\
/user/work/tk19812/software/ntLink-1.3.8/bin/ntlink_overlap_sequences.py -m -  --path DraftGenome.cut250.tigmint.fa.k24.w150.z1000.stitch.path \
-s DraftGenome.cut250.tigmint.fa -d DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot -p DraftGenome.cut250.tigmint.fa.k24.w150.z1000 -g 20 -k 15 --outgap 0 --trim_info'
indexlr 1.4.9: Using more than 5 threads does not scale, reverting to 5.
Assessing putative overlaps...
Parameters for overlap stage:
    -m -
    -f 0.5
    -a DraftGenome.cut250.tigmint.fa.k24.w150.z1000.stitch.path
    -s DraftGenome.cut250.tigmint.fa
    -k 15
    -d DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot
    -g 20
    --outgap 0
    -p DraftGenome.cut250.tigmint.fa.k24.w150.z1000
2024-02-24 11:56:18.000548 : Reading fasta file DraftGenome.cut250.tigmint.fa
2024-02-24 11:56:18.626472 : Reading scaffold file DraftGenome.cut250.tigmint.fa.k24.w150.z1000.n2.scaffold.dot
2024-02-24 11:56:18.628538 : Finding valid minimizer regions
2024-02-24 11:56:18.629266 : Finding scaffold overlaps
2024-02-24 11:56:19.592893 : Printing trimmed scaffolds
2024-02-24 11:56:20.735115 : DONE!
MergeContigs -k2 DraftGenome.cut250.tigmint.fa.k24.w150.z1000.trimmed_scafs.fa DraftGenome.cut250.tigmint.fa.k24.w150.z1000.trimmed_scafs.path > DraftGenome.cut250.tigmint.fa.k24.w150.z1000.stitch.abyss-scaffold.fa
The minimum coverage of single-end contigs is inf.
The minimum coverage of merged contigs is inf.
ln -sf DraftGenome.cut250.tigmint.fa.k24.w150.z1000.stitch.abyss-scaffold.fa DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.fa
echo "Done ntLink! Final post-ntLink scaffolds can be found in: DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.fa"
Done ntLink! Final post-ntLink scaffolds can be found in: DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.fa
make[1]: Leaving directory `/user/work/tk19812/HoneyPotProject/ONTREADS/Mbag.0.7.FlyeGenome'
ln -sf DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.fa DraftGenome.k24.w150.tigmint-ntLink.longstitch-scaffolds.fa
echo "Done LongStitch steps Tigmint-long and ntLink! Scaffolds can be found in: DraftGenome.k24.w150.tigmint-ntLink.longstitch-scaffolds.fa"
Done LongStitch steps Tigmint-long and ntLink! Scaffolds can be found in: DraftGenome.k24.w150.tigmint-ntLink.longstitch-scaffolds.fa
arcs-make arks-long draft=DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds reads=ont_reads m=8-10000 cut=250 j=0.05 k=20 l=4 c=4 a=0.3 D=true z=1000
make[1]: Entering directory '/user/work/tk19812/HoneyPotProject/ONTREADS/Mbag.0.7.FlyeGenome'
perl -ne 'chomp; if(/>/){$ct+=1; print ">$ct\n";}else{print "$_\n";} ' < DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.fa > DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.renamed.fa 
touch empty.fof
/user/work/tk19812/.conda/envs/longstitch/bin/share/arcs-1.2.5-0/bin//../src/long-to-linked-pe -l 250 -t 8 -m2000 ont_reads.fasta.gz |\
arcs --arks -v -D -B 20 -f DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.renamed.fa -c 4 -m 8-10000 -r 0.05 -e 30000 -z 1000 -j 0.05 -k 20 -t 8 -d 0 --gap 100 -b DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000 -u ont_reads.barcode-multiplicity.tsv /dev/stdin
long-to-linked-pe v1.0: Using more than 6 threads does not scale, reverting to 6.
Reading user inputs...
Finished reading user inputs...entering runArcs()...
Running: arcs 1.2.5
ARKS method
 pid 80655
 -c 4
 -d 0
 -e 30000
 -l 0
 -m 8-10000
 -r 0.05
 -v 1
 -z 1000
 --gap=100
 -k 20
 -j 0.05
 -t 8
 -b DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000
 -g DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000.dist.gv
 --barcode-counts=NA
 --tsv=DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000_main.tsv
 -a NA
 -f DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.renamed.fa
 -u ont_reads.barcode-multiplicity.tsv
 /dev/stdin

=>Preprocessing: Gathering barcode multiplicity information...Sat Feb 24 11:56:22 2024
pigz: skipping: ont_reads.fasta.gz unrecognized format
[2024-02-24 11:56:22][ERROR] A helper process has finished unsuccessfully:
PID: 80660
Outcome: exited with status 1
[2024-02-24 11:56:22][WARNING] ont_reads.fasta.gz is empty.
[2024-02-24 11:56:22][ERROR] Process pipeline: Spawner process failed.
Saw 30149  distinct barcodes.

=>Preprocessing: Gathering draft information...Sat Feb 24 11:56:22 2024

Number of contigs:2258
Size of Contig Array:4517

=>Storing Kmers from Contig ends... Sat Feb 24 11:56:23 2024

Finished 1000 Contigs...
Finished 2000 Contigs...
Finished 3000 Contigs...
Finished 4000 Contigs...
Total number of contigs in draft genome:  4700
Total valid contigs:  2258
Total skipped contigs:  2442
Total number of Kmers:  21096489
Number Null Kmers:  842
Number Kmers Recorded:  11313265
Number Kmer Collisions:  9783224
Number Times Kmers Removed (since duplicate in different contig):  9506595
Number of unique kmers (only one contig):  9136651

=>Reading Chromium FASTQ file(s)... Sat Feb 24 11:56:44 2024

Reading chrom /dev/stdin
File /dev/stdin opened.
Stored read pairs: 0
Skipped invalid read pairs: 0
Skipped unpaired reads: 0
Skipped reads pairs without a good contig: 0
Total valid kmers: 0
Number invalid kmers: 0
Number of kmers found in ContigKmap: 0
Number of kmers recorded in Ktrack: 0
Number of kmers found in ContigKmap but duplicate: 0
Number of reads passing jaccard threshold: 0
Number of reads failing jaccard threshold: 0
Cumulative memory usage: 490120

=> Pairing scaffolds... Sat Feb 24 11:56:44 2024

=> Creating the graph... Sat Feb 24 11:56:44 2024

=> Calculating distance estimates... Sat Feb 24 11:56:44 2024

    => Measuring intra-contig distances / shared barcodes... Sat Feb 24 11:56:44 2024

    => Writing intra-contig distance samples to TSV... Sat Feb 24 11:56:44 2024

    => Building Jaccard to distance map... Sat Feb 24 11:56:44 2024

    => Calculating barcode stats for scaffold pairs... Sat Feb 24 11:56:44 2024

    => Adding edge distances... Sat Feb 24 11:56:44 2024

=> Writing graph file... Sat Feb 24 11:56:44 2024

      Max Degree (-d) set to: 0. Will not delete any vertices from graph.
      Writing graph file to DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000_original.gv...

=> Creating the ABySS graph... Sat Feb 24 11:56:44 2024

=> Writing the ABySS graph file... Sat Feb 24 11:56:44 2024

{ "All_barcodes_unfiltered":30149, "All_barcodes_filtered":30149, "Scaffold_end_barcodes":0, "Min_barcode_reads_threshold":8, "Max_barcode_reads_threshold":10000 }

=> Writing TSV file... Sat Feb 24 11:56:44 2024

=> Done.
Sat Feb 24 11:56:44 2024
make[1]: *** [/user/home/tk19812/.conda/envs/longstitch/bin/share/arcs-1.2.5-0/bin/arcs-make:303: DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000_original.gv] Error 141
make[1]: *** Deleting file 'DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000_original.gv'
make[1]: Leaving directory '/user/work/tk19812/HoneyPotProject/ONTREADS/Mbag.0.7.FlyeGenome'
make: *** [DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000_l4_a0.3.scaffolds.fa] Error 2
lcoombe commented 8 months ago

Hi @francicco,

Ok, so I see this error in the log:

pigz: skipping: ont_reads.fasta.gz unrecognized format
[2024-02-24 11:56:22][ERROR] A helper process has finished unsuccessfully:
PID: 80660

I see a couple of other things that look funny - In Tigmint, it looks like it's using ont_reads.fasta, but in ntLink/ARKS, it's using ont_reads.fasta.gz?

/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/tigmint_estimate_dist.py ont_reads.fasta -n 1000000 -o ont_reads.tigmint-long.params.tsv
sh -c '/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/../src/long-to-linked-pe -l 250 -m2000 -g250000000 -s -b ont_reads.barcode-multiplicity.tsv --bx -t8 --fasta -f ont_reads.tigmint-long.params.tsv ont_reads.fasta | \
minimap2 -y -t8 -x map-ont --secondary=no DraftGenome.fa - | \
/user/home/tk19812/.conda/envs/longstitch/bin/share/tigmint-1.2.9-0/bin/tigmint_molecule_paf.py -q0 -s2000 -p ont_reads.tigmint-long.params.tsv - | sort -k1,1 -k2,2n -k3,3n  > DraftGenome.ont_reads.cut250.molecule.size2000.distauto.bed'
/user/work/tk19812/.conda/envs/longstitch/bin/share/arcs-1.2.5-0/bin//../src/long-to-linked-pe -l 250 -t 8 -m2000 ont_reads.fasta.gz |\
arcs --arks -v -D -B 20 -f DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds.renamed.fa -c 4 -m 8-10000 -r 0.05 -e 30000 -z 1000 -j 0.05 -k 20 -t 8 -d 0 --gap 100 -b DraftGenome.cut250.tigmint.fa.k24.w150.z1000.ntLink.scaffolds_c4_m8-10000_cut250_k20_r0.05_e30000_z1000 -u ont_reads.barcode-multiplicity.tsv /dev/stdin

Which is the file that you're intending to use?

If the file is ont_reads.fasta.gz, try updating your longstitch installation, including the Tigmint dependency. It looks like you are using Tigmint v1.2.9, but the release v1.2.10 is the one that supports fasta.gz format (https://github.com/bcgsc/tigmint/releases/tag/v1.2.10)

Thank you for your interest in LongStitch! Lauren

github-actions[bot] commented 6 months ago

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