Comments (6)
Hi @xiekunwhy
This is strange. My guess is that the short read were not properly assembled by Minia in the first place.
Can you please also share the size of files in the parent directory of the one you have shared?
Also, what is the expected size of the genome?
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Hi,
The expected genome size is ~3.2G accorrding to FCM results, but it is a high heterouzygous genome(only heterouzygous peak in kmer curve plot).
The following is the file sizes in the parent directory, any suggestions?
from haslr.
Hi folks, any progress with this issue? I'm facing the same problem - an example (quick start) works well, but with real data (Illumina + ONT) conda and source code versions produce an empty final assembly. No errors during the compilation have raised.
checking /software/conda-modules/5.3.1/envs/haslr/bin/haslr_assemble: ok checking /software/conda-modules/5.3.1/envs/haslr/bin/minia_nooverlap: ok checking /software/conda-modules/5.3.1/envs/haslr/bin/fastutils: ok checking /software/conda-modules/5.3.1/envs/haslr/bin/minia: ok checking /software/conda-modules/5.3.1/envs/haslr/bin/minimap2: ok number of threads: 8 output directory: /scratch/vorel/job_138582.elixir-pbs.elixir-czech.cz/ver_1_out subsampling 25x long reads to /scratch/vorel/job_138582.elixir-pbs.elixir-czech.cz/ver_1_out/lr25x.fasta... done assembling short reads using Minia... done removing overlaps in short read assembly... done removing short sequences in short read assembly... done aligning long reads to short read assembly using minimap2... done assembling long reads using HASLR... done
haslr.py -t 8 -o ver_1_out -g 50m -l run1_2_merge_trim.fastq -x nanopore --aln-sim 0.80 -s Ktang_Tang_1_trim_paired_dedup_cor.fastq Ktang_Tang_2_trim_paired_dedup_cor.fastq Ktang_Tang_1_trim_unpaired_dedup_cor.fastq Ktang_Tang_2_trim_unpaired_dedup_cor.fastq
from haslr.
I have the same problem when trying to run a similar pipeline, does anyone has a solution ?
from haslr.
same here
from haslr.
same here, the final assembly fasta does not even exist
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 asm.final.ann
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.01.init.gfa
-rw-r--r-- 1 hoelzerm domänen-benutzer 42 Jun 10 09:32 backbone.01.init.stat
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.02.weakEdge.gfa
-rw-r--r-- 1 hoelzerm domänen-benutzer 42 Jun 10 09:32 backbone.02.weakEdge.stat
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.03.tip.gfa
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.03.tip.log
-rw-r--r-- 1 hoelzerm domänen-benutzer 42 Jun 10 09:32 backbone.03.tip.stat
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.04.simplebubble.gfa
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.04.simplebubble.log
-rw-r--r-- 1 hoelzerm domänen-benutzer 42 Jun 10 09:32 backbone.04.simplebubble.stat
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.05.superbubble.gfa
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.05.superbubble.log
-rw-r--r-- 1 hoelzerm domänen-benutzer 42 Jun 10 09:32 backbone.05.superbubble.stat
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.06.smallbubble.log
-rw-r--r-- 1 hoelzerm domänen-benutzer 42 Jun 10 09:32 backbone.06.smallbubble.stat
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.branching.log
-rw-r--r-- 1 hoelzerm domänen-benutzer 4 Jun 10 09:32 compact_uniq.txt
-rw-r--r-- 1 hoelzerm domänen-benutzer 7.3M Jun 10 09:32 index.contig
-rw-r--r-- 1 hoelzerm domänen-benutzer 41K Jun 10 09:32 index.longread
-rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 log_asmfinal.txt
but it seems the short-read assembly worked
-rw-r--r-- 1 hoelzerm domänen-benutzer 44M Jun 10 09:32 sr_k49_a3.unitigs.fa
I expect ~40Mb
from haslr.
Related Issues (20)
- speed running HOT 14
- assembling long reads using HASLR... failed ERROR HOT 9
- Debug Message in log File
- Bug while running script: "could not find file"
- Short Homo Sapien Assembly from Genome in a Bottle Data HOT 10
- Multiple long read files in the latest version
- Changing K-mer size of Minia leads to final fasta of zero bits
- Failing while checking minia
- question multiple libraries?
- Does this tool do phasing?
- kmer determination
- Much Shorter Assembly than Expected HOT 1
- AttributeError: 'module' object has no attribute 'run' HOT 1
- lr0x.fasta... [ERROR] option -d/--depth is required HOT 1
- new release for bioconda
- Assembling pacbio, nanopore and illumina reads HOT 2
- ERROR: "haslr_assemble" returned non-zero exit status
- Clean raw data prior to assembly
- Assembling the test data does not generate an assembly HOT 2
- final.fa is 0 kb HOT 2
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