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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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defining an output file #184

Open Sabrin2020 opened 10 months ago

Sabrin2020 commented 10 months ago

Hi all, I have difficulty defining an output file for my relative abundance run, any hints please what am I missing here? 

coverm genome --genome-fasta-extension fasta  --genome-fasta-files *.fa \
> -t 24    \
> -1  *-FILTERED_R1.fastq.gz \
> -2  *-FILTERED_R1.fastq.gz --output-format dense \
> --min-read-percent-identity 95 \
> --min-read-aligned-percent 75 -o Bur_relative_abundance.tsv
error: Found argument '-o' which wasn't expected, or isn't valid in this context

USAGE:
    coverm genome --coupled <coupled>... --genome-definition <genome-definition> --genome-fasta-directory <genome-fasta-directory> --genome-fasta-extension <genome-fasta-extension> --genome-fasta-files <genome-fasta-files>... --interleaved <interleaved>... --min-read-aligned-percent <min-read-aligned-percent> --min-read-percent-identity <min-read-percent-identity> --output-format <output-format> -1 <read1>... -2 <read2>... --separator <separator> --single <single>... --threads <threads>

For more information try --help
wwood commented 10 months ago

Hi,

What version is this?

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: Sabrin2020 @.> Sent: Thursday, August 31, 2023 2:03:44 AM To: wwood/CoverM @.> Cc: Subscribed @.***> Subject: [wwood/CoverM] defining an output file (Issue #184)

Hi all, I have difficulty defining an output file for my relative abundance run, any hints please what am I missing here?

coverm genome --genome-fasta-extension fasta --genome-fasta-files *.fa \

-t 24 \ -1 -FILTERED_R1.fastq.gz \ -2 -FILTERED_R1.fastq.gz --output-format dense \ --min-read-percent-identity 95 \ --min-read-aligned-percent 75 -o Bur_relative_abundance.tsv error: Found argument '-o' which wasn't expected, or isn't valid in this context

USAGE: coverm genome --coupled ... --genome-definition --genome-fasta-directory --genome-fasta-extension --genome-fasta-files ... --interleaved ... --min-read-aligned-percent --min-read-percent-identity --output-format -1 ... -2 ... --separator --single ... --threads

For more information try --help

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Sabrin2020 commented 10 months ago

conda create -n coverm -c bioconda coverm conda activate coverm conda install -c bioconda coverm


[2023-08-30T10:18:27Z INFO  coverm] CoverM version 0.4.0
[2023-08-30T10:18:27Z INFO  coverm] Using min-covered-fraction 10%
[2023-08-30T10:18:27Z INFO  bird_tool_utils::external_command_checker] Found minimap2 version 2.22-r1101
[2023-08-30T10:18:28Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.9
wwood commented 10 months ago

It seems you are running an out of date version, which is the cause. Try updating.

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

From: Sabrin2020 @.> Sent: Thursday, August 31, 2023 2:34:46 AM To: wwood/CoverM @.> Cc: Ben J Woodcroft @.>; Comment @.> Subject: Re: [wwood/CoverM] defining an output file (Issue #184)

[2023-08-30T10:18:27Z INFO coverm] CoverM version 0.4.0 [2023-08-30T10:18:27Z INFO coverm] Using min-covered-fraction 10% [2023-08-30T10:18:27Z INFO bird_tool_utils::external_command_checker] Found minimap2 version 2.22-r1101 [2023-08-30T10:18:28Z INFO bird_tool_utils::external_command_checker] Found samtools version 1.9

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Sabrin2020 commented 10 months ago

I tried to update , I uninstalled and reinstalled from here https://anaconda.org/bioconda/coverm but ended up with same version. How can I install latest version with conda please?

wwood commented 10 months ago

Try making a new environment, or installing with install coverm==0.6.1

franlat commented 9 months ago

I had the same issue: using conda install -c bioconda coverm would install version 0.4.0 by default, and installing version 0.6.1 raised an error. However, I stated the order of the channels (conda-forge > bioconda) and then it worked like a charm: conda install -c conda-forge -c bioconda coverm=0.6.1.

Sabrin2020 commented 9 months ago

@franlat thank you so much it works