Comments (11)
According to the log, the error appears to actually be in the igdiscover_igblast
rule. If the below doesn’t fix the issue, can you show the contents of the file /lustre/home/acct-medsn/medsn/IMQ1_BCR/.snakemake/log/2023-07-06T155201.795624.snakemake.log
mentioned in the very last line of the log?
Regading barcodes/UMIs: What IgDiscover calls "barcode" is actually the UMI, so your thinking is correct. However, IgDiscover expects the UMI to be at the 5' end of the read, so if you set barcode_length_5prime
to 10, the first 10 bases of the 10X barcode would be interpreted as the UMI. I think this would mean that all reads from one GEM would be merged into a single one by IgDiscover. This might even explain the above igdiscover_igblast
error.
My suggestion is to try setting barcode_length_5prime
to 26 to make IgDiscover treat the combined 10X barcode plus UMI as UMI. (Disclaimer: I have not used IgDiscover myself with 10X data.)
from igdiscover-legacy.
According to the log, the error appears to actually be in the
igdiscover_igblast
rule. If the below doesn’t fix the issue, can you show the contents of the file/lustre/home/acct-medsn/medsn/IMQ1_BCR/.snakemake/log/2023-07-06T155201.795624.snakemake.log
mentioned in the very last line of the log?Regading barcodes/UMIs: What IgDiscover calls "barcode" is actually the UMI, so your thinking is correct. However, IgDiscover expects the UMI to be at the 5' end of the read, so if you set
barcode_length_5prime
to 10, the first 10 bases of the 10X barcode would be interpreted as the UMI. I think this would mean that all reads from one GEM would be merged into a single one by IgDiscover. This might even explain the aboveigdiscover_igblast
error.My suggestion is to try setting
barcode_length_5prime
to 26 to make IgDiscover treat the combined 10X barcode plus UMI as UMI. (Disclaimer: I have not used IgDiscover myself with 10X data.)
Thanks for your reply. And I've tried to corrected the barcode_length_5prime
to 26 but it didn't fix my issue. I still got the problem. and i've attached the log file here.
2023-07-07T095124.994995.snakemake.log
from igdiscover-legacy.
hello,i've updated my issue and i'm waiting for your reply. Thanks!
from igdiscover-legacy.
Can you please run igdiscover igblastwrap --sequence-type=Ig --threads=16 iteration-01/database reads/sequences.fasta.gz > /dev/null
and paste the output here? There should be an error message.
from igdiscover-legacy.
Thanks! I ran the commands and got the following output.
INFO: Running IgBLAST on input reads
Traceback (most recent call last):
File "/lustre/home/acct-medsn/medsn/.conda/envs/igdiscover/bin/igdiscover", line 10, in
sys.exit(main())
File "/lustre/home/acct-medsn/medsn/.conda/envs/igdiscover/lib/python3.10/site-packages/igdiscover/main.py", line 92, in main
to_run()
File "/lustre/home/acct-medsn/medsn/.conda/envs/igdiscover/lib/python3.10/site-packages/igdiscover/main.py", line 90, in
to_run = lambda: module.main(args)
File "/lustre/home/acct-medsn/medsn/.conda/envs/igdiscover/lib/python3.10/site-packages/igdiscover/cli/igblastwrap.py", line 122, in main
"Processed {:10,d} sequences at {:.1f} ms/sequence".format(n, elapsed / n * 1e3)
ZeroDivisionError: float division by zero
from igdiscover-legacy.
Thanks, that is helpful. It appears that no reads remain after preprocessing. That is, IgBLAST works on zero input sequences. There are a couple of preprocessing steps and it is unclear to me at the moment which one filters out all reads. What are the contents of reads/2-pear.log
?
from igdiscover-legacy.
I uploaded the log file here.
2-pear.log
from igdiscover-legacy.
Ok, that step went fine. What are the contents of the files stats/trimmed.json
and stats/groups.json
?
from igdiscover-legacy.
... and of reads/4-sequences.fasta.gz.log
?
from igdiscover-legacy.
it seemed that all sequences were trimmed.
groups.json:
{
"unique_barcodes": 0,
"barcode_singletons": 0,
"groups_written": 0,
"group_size_1": 0,
"group_size_2": 0,
"group_size_3plus": 0
}
and trimmed.json:
{"trimmed": 21081671}
from igdiscover-legacy.
The large number in trimmed.json
is actually the number of sequences remaining after trimming, so it is good that it is high. ("Trimming" actually refers to primer removal, but since you haven’t configured any primers in your configuration, no trimming is done anyway.)
The problem appears to be in the "grouping" step where IgDiscover mainly groups together sequences that have the same UMI, but it also does some minor filtering. In particular, it filters out sequences that are too short, and it seems that in your case, it considers all sequences to be too short:
INFO: 21081671 sequences in input
INFO: 0 sequences long enough
Your configuration file has this:
minimum_merged_read_length: 300
So it appears that all your sequences end up as being shorter than 300 bp.
What is actually the read length of your 10X reads? Maybe the data isn’t suitable for IgDiscover.
from igdiscover-legacy.
Related Issues (20)
- Parse Flash stats fails HOT 3
- Error: No V genes were discovered in this iteration HOT 11
- Docs may need updating for J discovery HOT 2
- Where is the complete germline DataBase? HOT 1
- Error in rule read_length_histogram HOT 3
- Snakemake workflow problem with symlinks and temp() HOT 4
- Give sensible error message when running init without DISPLAY
- snakemake error HOT 12
- IgDiscover crashes if no arguments are given HOT 1
- Error running against the test data set HOT 3
- IgBlast error HOT 1
- length of CDR1 region is not divisible by three HOT 3
- Complain if the input reads contain non-nucleotide characters/spaces HOT 10
- error about Microsoft Visual C++ on installation HOT 1
- Solving environment: failed HOT 2
- Cannot install IgDiscover on M1 MacBook Pro HOT 3
- IgDiscover crashes with pandas 2.0.0 HOT 5
- trouble installing with conda HOT 2
- New IgDiscover repository
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 igdiscover-legacy.