[ERRORS] A helper process has finished unsuccessfully and Process pipeline: Spawner process failed.
francicco opened this issue · 2 comments
francicco commented
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
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 commented
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in LongStitch!