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A pipeline for detecting mis-assemblies in metagenomic assemblies.

License: MIT License

Python 44.52% Makefile 0.08% TeX 50.07% R 1.76% Shell 3.57%

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valet's Issues

use only a single thread for samtools sort

with -@ 16 I get samtools sort: couldn't allocate memory for bam_mem

also better on HPC systems where the resources need to be allocated precisely.

Feature request: gz as input, bam as input

I am having a look at VALET and I think it is a nice piece of code for checking a metagenome assembly. For me at least it would help if

I can give already mapped data as input (bam files)
support gzipped input

wrong repo name in readme

should be git clone https://github.com/jgluck/VALET.git not git clone https://github.com/jgluck/VALET.git

generate summary table fails

I am validating a metagenomic assembly with a single FASTA file of reads and keep getting this error. The contigs are numbered sequentially in the final assembly, e.g.:

>951_contig1
>951_contig2
...
>951_contig10682

Assembly here

The pipeline keeps failing when trying to generate the summary table. Full command and STDOUT are copied below. I am running (on a cluster):

Python 2.7.9
bowtie2 2.2.4
samtools 1.2
numpy 1.9.3
bedtools 2.24

$ python ~/Software/cmhill_VALET/src/py/valet.py -a 951.final.renamed.headers.fasta -r ../02-pear/951pear.assembled.fasta
###########################################################################
PROCESSING ASSEMBLY: asm_0 (951.final.renamed.headers.fasta)
###########################################################################
COMMAND:     reapr facheck 951.final.renamed.headers.fasta output/asm_0/assembly_facheck
RESULTS:     output/asm_0/assembly_facheck
---------------------------------------------------------------------------
STEP:    FILTERING ASSEMBLY CONTIGS LESS THAN 1000 BPs
RESULTS:     output/asm_0/filtered_assembly.fasta
---------------------------------------------------------------------------
STEP:    ALIGNING READS
COMMAND:     bowtie2-build /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/output/asm_0/filtered_assembly.fasta /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/output/asm_0/indexes/temp_2ucgDE
COMMAND:     bowtie2 -a -x /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/output/asm_0/indexes/temp_2ucgDE -q -U ../02-pear/951pear.assembled.fasta --very-sensitive -a --reorder -p 8 --un /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/output/asm_0/unaligned_reads/unaligned.reads -S output/asm_0/sam/library.sam
---------------------------------------------------------------------------
STEP:    RUNNING SAMTOOLS
COMMAND:     samtools view -F 0x100 -bS output/asm_0/sam/library.sam
COMMAND:     samtools sort output/asm_0/bam/library.bam output/asm_0/bam/sorted_library
COMMAND:     samtools mpileup -C50 -A -f output/asm_0/filtered_assembly.fasta output/asm_0/bam/sorted_library.bam
RESULTS:     output/asm_0/coverage/mpileup_output.out
COMMAND:     samtools index output/asm_0/bam/sorted_library.bam
---------------------------------------------------------------------------
STEP:    CALCULATING CONTIG COVERAGE
RESULTS:     output/asm_0/coverage/temp.cvg
---------------------------------------------------------------------------
STEP:    PARTITIONING COVERAGE FILE
COMMAND:     /home/bonddr/badalame/Software/cmhill_VALET/src/py/split_pileup.py -p output/asm_0/coverage/mpileup_output.out -c 8
---------------------------------------------------------------------------
STEP:    DEPTH OF COVERAGE
COMMAND:     /home/bonddr/badalame/Software/cmhill_VALET/src/py/depth_of_coverage.py -m output/asm_0/coverage/mpileup_output.out -w 501 -o output/asm_0/coverage/errors_cov.bed -g -e -c 8
COMMAND:     bedtools sort -i output/asm_0/coverage/errors_cov.bed
Error: The requested file (output/asm_0/coverage/errors_cov.bed) could not be opened. Error message: (No such file or directory). Exiting!
RESULTS:     output/asm_0/coverage.bed
---------------------------------------------------------------------------
STEP:    BREAKPOINT
COMMAND:     /home/bonddr/badalame/Software/cmhill_VALET/src/py/breakpoint_splitter.py -u /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/output/asm_0/unaligned_reads/ -o output/asm_0/breakpoint/split_reads/
COMMAND:     /home/bonddr/badalame/Software/cmhill_VALET/src/py/breakpoint_finder.py -a output/asm_0/filtered_assembly.fasta -r output/asm_0/breakpoint/split_reads/ -b 50 -o output/asm_0/breakpoint/ -c output/asm_0/coverage/temp.cvg -p 8
COMMAND:     bedtools sort -i output/asm_0/breakpoint/interesting_bins.bed
Error: The requested file (output/asm_0/breakpoint/interesting_bins.bed) could not be opened. Error message: (No such file or directory). Exiting!
RESULTS:     output/asm_0/breakpoint/../breakpoints.bed
---------------------------------------------------------------------------
STEP:    SUMMARY
RESULTS:     output/asm_0/summary.bed
RESULTS:     output/asm_0/suspicious.bed
Traceback (most recent call last):
  File "/home/bonddr/badalame/Software/cmhill_VALET/src/py/valet.py", line 1169, in <module>
    main()
  File "/home/bonddr/badalame/Software/cmhill_VALET/src/py/valet.py", line 239, in main
    contig_lengths, contig_abundances, final_misassemblies)
  File "/home/bonddr/badalame/Software/cmhill_VALET/src/py/valet.py", line 1008, in generate_summary_table
    table_file.write(contig + '\t' + str(filtered_contig_lengths[contig]) + '\t' + str(contig_abundances[contig]) + '\t' + \
KeyError: '951_contig6066'

Release?

Hi,

I would like to create a Bioconda recipe for your tool. It would be easier if there is a release of the tool. Is it possible for you to create one?

Thanks a lot,

Bérénice

parameter -q for reads as fastq bug

Using parameter -q indicates reads are fastq format with fasta as default. I believe VALET treats the reads as fastq by default, and likely requires reads in fastq format. Using the -q parameter causes and error with breakpoint finder. Proposed solution is to remove the -q parameter from the options and require fastq file as input.

Assembly correction

Hello,

Are you continue to develop VALET? I haven't seen any publication for it yet only the thesis.
Do you think it is possible to use VALET automatically correct assembly? This will mean mostly split an assembly at a breakpoint and may be at the edges of low-density regions.

Did you do a systematic review of the misassemblies detected by quast and VALET?
I would like to contribute.

Kind regards
Silas Kieser

VALET available as conda package

Hi,

VALET is now available as a conda package: https://bioconda.github.io/recipes/valet/README.html
If you want, I can open a Pull Request here to update the README file to add how to install Nonpareil using conda and also the badge:

Berenice

Metagenome assembly?

Can VALET be used to evaluate metagenome assemblies i.e. just a contigs file (without binning)?

Regards,
Aditya

SyntaxError: invalid syntax

After installing the program according to instructions provided here I try a run with the test data and get the following error:

src/py/valet.py --skip-reapr -a test/c_rudii_reference.fna,test/c_rudii_dup.fna,test/c_rudii_relocation.fna,test/c_rudii_reloc_dup.fna -1 test/lib1.1.fastq -2 test/lib1.2.fastq --assembly-names reference,duplication,relocation,reloc-dup
  File "src/py/valet.py", line 854
    with open(bin_path + '/reapr/03.score.errors.gff', 'r') as reapr_gff, \
                                                                        ^
SyntaxError: invalid syntax

I am not sure why it is related to reapr, if I added "--skip-reapr" (I am not able to install REAPR in my machine).

Would you have any idea of the problem here?

Thank you in advance

VALET with Long reads

Hi @bebatut,

Mine is a general question. Is VALET suited for long-read data such as PacBio or nanopore? I would like a tool that would work as REAPR but for long-reads.

Thanks
Best,
F

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