defining an output file

[Sabrin2020]

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]

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 <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 ― Reply to this email directly, view it on GitHub<#184>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5FQ4VIGP3MYHIAQQFTXX5P6BANCNFSM6AAAAAA4EYB5DY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Sabrin2020]

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]

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 ― Reply to this email directly, view it on GitHub<#184 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5FGUL74CFM2YDJPMMDXX5TSNANCNFSM6AAAAAA4EYB5DY>. You are receiving this because you commented.Message ID: ***@***.***>

[Sabrin2020]

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]

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

[franlat]

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]

@franlat thank you so much it works