dyxstat/hicbin

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

hicbin's Issues

How to get the TAX_file

Dear sir,
I am using HiCBin to process my data, but the software TAXAassign does not work for me. Could you suggest any other method to get the TAX_file? Thanks.

TypeError during "Generating contig labels..."

Hi,

I would like to ask you for a help with this error. All files were prepared as you recommended in documentation. Only one difference is that my bam file is merged file of two bam files and coverage was calculate from the merged file.

INFO | 2023-03-16 19:53:23,043 | contact_matrix | Reading fasta file...
Analyzing contigs in reference fasta: 100%|██████████████████████████████████████████████████████████████| 59145/59145 [00:13<00:00, 4464.22it/s]
INFO | 2023-03-16 19:53:44,824 | contact_matrix | Generating contig labels...
Traceback (most recent call last):
File "./hicbin.py", line 196, in
min_signal=ifelse(args.min_signal, runtime_defaults['min_signal']))
File "/home/sehnal/HiCBin/contact_matrix.py", line 591, in init
self._generate_tax()
File "/home/sehnal/HiCBin/contact_matrix.py", line 715, in _generate_tax
taxlist = taxaassignMat[: , 1:].sum(1) #taxassign name
File "/home/sehnal/miniconda3/envs/HiCBin_env/lib/python3.7/site-packages/numpy/core/_methods.py", line 47, in _sum
return umr_sum(a, axis, dtype, out, keepdims, initial, where)
TypeError: can only concatenate str (not "float") to str

Thanks for reply,
Ludek

TAXAassign can't be installed.

HiCBin assign taxonomy to contigs by TAXAassign. But we can hardly install TAXAassign, can we use alternative tools, such as Kraken2(https://ccb.jhu.edu/software/kraken2/) or mmseqs2(https://github.com/soedinglab/mmseqs2/wiki#taxonomy-assignment)?
Could you please give me some suggestion? Thank you!

Trouble installing glmmTMB package in R in conda environment

Hi,

After activating the conda environment, opening up R and then running the "install.packages("glmmTMB", type="source")" command, it seems that R has trouble finding the C compiler within the conda environment for all of the dependencies for glmmTMB in R. Here is the error message for each package:

* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-conda-linux-gnu-cc -I"/home/jamestan/.conda/envs/HiCBin_env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jamestan/.conda/envs/HiCBin_env/include -I/home/jamestan/.conda/envs/HiCBin_env/include -Wl,-rpath-link,/home/jamestan/.conda/envs/HiCBin_env/lib  -Iutf8lite/src -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jamestan/.conda/envs/HiCBin_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1611775910217/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/home/jamestan/.conda/envs/HiCBin_env=/usr/local/src/conda-prefix  -c as_utf8.c -o as_utf8.o
x86_64-conda-linux-gnu-cc: fatal error: cannot execute 'cc1': execvp: No such file or directory
compilation terminated.
make: *** [/home/jamestan/.conda/envs/HiCBin_env/lib/R/etc/Makeconf:174: as_utf8.o] Error 1
ERROR: compilation failed for package ‘utf8’

I've tried updating to a more recent version of conda (23.1.0) but that doesn't seem to fix it either. Wondering if you had any thoughts on how to move forward.

Thanks!

error on 'Normalizing raw contacts by HiCzin'

Dear sir,

When I using HiCzin, I got an error on the step 'Normalizing raw contacts by HiCzin'. The log file and current output files can be found here. Thanks!

valid_contact.csv.txt

hicbin.log

contig_info.csv.txt

coverage file index error

Hi, hope you are well. I met this below error. Any ideas? Thanks in advance.

File "/home/HiCBin/contact_matrix.py", line 584, in init
cov = cov.values[0: , [0,2]]
IndexError: index 2 is out of bounds for axis 1 with size

question about how to get the tax_file?

Dear sir,
I am using HiCBin to process my data, I want to use the TAXAassign to get the labels,but I get the following error after install the TAXAassign.

The follow is my software version:

python=2.7.18
blast=2.13.0
mysql=5.7.40
perl=5.26.1

Although at the beginning I ran the program and reported the following error due to perl version problem:

. Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/jianchang/software/TAXAassign/scripts/blast_gen_assignments.pl line 108

But I have modified the blast_gen_assignments.pl file to fit this version
Can you give me some advice? Thank you!

Empty contact matrix

Hi,
Thank you so much for the tool.
On running the tool, it exits with the log message
The output directory contains exmpty files

INFO | 2024-02-05 15:21:46,996 | contact_matrix | Filtering contigs according to minimal signal(2)...
INFO | 2024-02-05 15:21:46,997 | contact_matrix | Generating intra-species contig pairs...
INFO | 2024-02-05 15:21:46,997 | contact_matrix | Writing valid intra-species contacts...
INFO | 2024-02-05 15:21:46,998 | contact_matrix | Writing acceptable contig information...
INFO | 2024-02-05 15:21:46,998 | main | Stopping as the contact matrix is empty

commnand:python hicbin.py pipeline contig_assembly_test.fa align_test.bam contig_tax_test.csv coverage_test.txt out_1

Assuming that the problem might be with my data, I tried running the code with the test data given on github, it yielded the same results as well.
Could you please help me with what might be the issue here?
Thanks in advance!

run jgi_summarize_bam_contig_depths error

when I run ./jgi_summarize_bam_contig_depths --outputDepth coverage410.txt --pairedContigs pair410.txt test/sorted.bam,I get an error Please execute 'samtools sort' on unsorted input bam files and try again! . But I have run the command samtools sort -o sorted.bam -n align_test.bam , I still make the mistake. I don't know what to do. I would appreciate it if you could give me some advice. Thank you!