Comments (10)
@programmingprincess The current version of HATCHet is now supporting any reference genome; in particular, now binBAM
is provided directly with the reference genome itself (which is required to be properly indexed) and the size of the chromosomes are read from the corresponding dictionary (as default, same name of the indexed reference with .dict
extension).
Please let us know if you can test the current version with your samples and reference genome and we keep the issue open for now.
from hatchet.
HATCHet can be applied with any reference genome of a diploid organism, however the current implementation needs to be aware of some details of the reference: in particular, it needs to know the length of the chromosomes in the reference. This is why there is a list of supported references. If you could please provide the name and the details of your reference genome (especially the chromosome lengths), I will be very happy to integrate immediately that reference among those supported.
from hatchet.
Thanks! I could not find the list of supported references. The reference genome I am working with is sus scrofa 11.1
from hatchet.
We are gonna release a new version in the next couple of days which will automatically support any reference genome, without the need to specify the name.
I will update this post as soon as it will be released
from hatchet.
@simozacca Just tested the current version with the reference genome, it looks good! Thanks for the follow up 👍
from hatchet.
Hello- thanks for the tool.
I am having trouble using this tool with a non-human reference. All in the same dir are : genome.fasta, genome.fasta.fai, and genome.dict.
I tried running the whole with a hatchet.ini file as discussed here:
http://compbio.cs.brown.edu/hatchet/script/README.html
hatchet run hatchet.ini
And I tried just
hatchet count-reads -N ${NORMAL} -T ${PRIME} -b 25kb -g ${REF} -j 16 -O XX -o XpX -t total_read.counts --verbose
Both give this error:
WARNING: a chromosome named either 1 or a variant of CHR1 cannot be found in the normal BAM file
WARNING: a chromosome named either 2 or a variant of CHR2 cannot be found in the normal BAM file
WARNING: a chromosome named either 3 or a variant of CHR3 cannot be found in the normal BAM file
WARNING: a chromosome named either 4 or a variant of CHR4 cannot be found in the normal BAM file
WARNING: a chromosome named either 5 or a variant of CHR5 cannot be found in the normal BAM file
WARNING: a chromosome named either 6 or a variant of CHR6 cannot be found in the normal BAM file
WARNING: a chromosome named either 7 or a variant of CHR7 cannot be found in the normal BAM file
WARNING: a chromosome named either 8 or a variant of CHR8 cannot be found in the normal BAM file
WARNING: a chromosome named either 9 or a variant of CHR9 cannot be found in the normal BAM file
WARNING: a chromosome named either 10 or a variant of CHR10 cannot be found in the normal BAM file
WARNING: a chromosome named either 11 or a variant of CHR11 cannot be found in the normal BAM file
WARNING: a chromosome named either 12 or a variant of CHR12 cannot be found in the normal BAM file
WARNING: a chromosome named either 13 or a variant of CHR13 cannot be found in the normal BAM file
WARNING: a chromosome named either 14 or a variant of CHR14 cannot be found in the normal BAM file
WARNING: a chromosome named either 15 or a variant of CHR15 cannot be found in the normal BAM file
WARNING: a chromosome named either 16 or a variant of CHR16 cannot be found in the normal BAM file
WARNING: a chromosome named either 17 or a variant of CHR17 cannot be found in the normal BAM file
WARNING: a chromosome named either 18 or a variant of CHR18 cannot be found in the normal BAM file
WARNING: a chromosome named either 19 or a variant of CHR19 cannot be found in the normal BAM file
WARNING: a chromosome named either 20 or a variant of CHR20 cannot be found in the normal BAM file
WARNING: a chromosome named either 21 or a variant of CHR21 cannot be found in the normal BAM file
WARNING: a chromosome named either 22 or a variant of CHR22 cannot be found in the normal BAM file
Traceback (most recent call last):
File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/bin/hatchet", line 33, in <module>
sys.exit(load_entry_point('hatchet==0.4.7', 'console_scripts', 'hatchet')())
File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/__main__.py", line 65, in main
globals()[command](args)
File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/utils/count_reads.py", line 16, in main
args = ap.parse_count_reads_arguments(args)
File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/utils/ArgParsing.py", line 277, in parse_count_reads_arguments
chromosomes = extractChromosomes(samtools, normal, samples)
File "/mnt/sequence/jurban/software/conda/anaconda3/envs/hatchet/lib/python3.7/site-packages/hatchet/utils/ArgParsing.py", line 520, in extractChromosomes
if len(chrm) == 0 and len(no_chrm) == 0: raise ValueError("No chromosomes found in the normal BAM")
ValueError: No chromosomes found in the normal BAM
I installed hatchet the following way:
conda create -n hatchet -c bioconda hatchet
conda activate hatchet
conda install tabix picard mosdepth
conda install shapeit -c dranew
conda install -c gurobi gurobi
Tell Ben I say hello. I knew him when he was at Brown, and sat in on some of his lab meetings.
from hatchet.
p.s. Im guessing the offending code is this:
505 def extractChromosomes(samtools, normal, tumors, reference=None):
506 # Read the names of sequences in normal BAM file
507 normal_sq = getSQNames(samtools, normal[0])
508
509 # Extract only the names of chromosomes in standard formats
510 chrm = set()
511 no_chrm = set()
512 for i in range(1, 23):
513 if str(i) in normal_sq:
514 no_chrm.add(str(i))
515 elif "chr" + str(i) in normal_sq:
516 chrm.add("chr" + str(i))
517 else:
518 sys.stderr.write("WARNING: a chromosome named either {} or a variant of CHR{} cannot be found in the normal BAM file\n".format(i, i))
519
520 if len(chrm) == 0 and len(no_chrm) == 0: raise ValueError("No chromosomes found in the normal BAM")
This appears to be hard-coded to expect human chromosomes.
I work with an insect - the chromosome names are: X, II, III, IV, and ....associated_contig_k... (for k in 1:N).
from hatchet.
Unfortunately the current version of HATCHet does not support genomes with different chromosome names than those in the human genome. Also, please note that HATCHet can only properly work with diploid genomes.
We will consider the extension in future developments, thank you!
from hatchet.
Thanks for letting me know. When you say "diploid genomes", are you referring to the ploidy of the organism or the assembly? The insect I work with is diploid (well it some cells polyploidize, but most somatic cells are diploid). The current assembly is collapsed into 1 haploid complement.
from hatchet.
I was referring to the ploidy of the organism; sorry I did not know that this insect was diploid. We think that we might be able to extend HATCHet to work with arbitrary chromosomes and we are working on it. Hopefully we might have new developments soon.
from hatchet.
Related Issues (20)
- tabix parse error and cluster-bins failure HOT 4
- Falling at plot-bin step, even after adjusting -tR and -tB
- Download 1000GP_Phase3
- Running HATCHet with phasing
- Failed to liftover chromosomes with picard
- Failed to parse the output of the following command because the final objective was not found: {cmd} HOT 2
- Full documentation is not in fact available from cs.brown.edu HOT 3
- Error in read_bb() in cluster_bins.py due to change in pandas df.groupby() HOT 4
- Error in plot_clusters() in plot_cn_1d2d.py due to change in pandas df.groupby() HOT 2
- Error when no reads are recorded in tumor.bed before/after centromere location HOT 2
- Specifying size for WES samples in count-reads HOT 1
- Set default value for ILP time limit
- can i ues this method for checking WGD of other species
- HATCHet2 RDR/BAF locally-aware clustering error with sparse bins
- String "None" is not converted to Python `None` object in `parse_combine_counts_args`
- Length of values does not match length of index
- resolve issue with CI testing python 3.7
- explore using more recent SHAPEIT version
- AssertionError at clustering step HOT 1
- add flag and make GC correction optional
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hatchet.