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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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-binners, just do maxbin #809

Closed laibinhuang closed 2 months ago

laibinhuang commented 3 months ago

when I use this flag:

-binners maxbin, metabat, concoct

I only see the pipeline does maxbin, not matabat and concoct bins

please help thank you,

jtamames commented 3 months ago

Enclose the binners between quotes, that is: -binners "maxbin,metabat,concoct"

fpusan commented 3 months ago

Just in case, what version of SqueezeMeta are you using and can you provide your syslog file?

laibinhuang commented 3 months ago

Yes, here it is!

Thank you, Laibin

Run started Thu Mar 7 11:56:21 2024 in coassembly mode

SqueezeMeta v1.6.3, September 2023 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 10.3389 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started for P21, Thu Mar 7 11:56:21 2024

On Fri, Mar 8, 2024 at 9:52 AM Fernando Puente-Sánchez < @.***> wrote:

Just in case, what version of SqueezeMeta are you using and can you provide your syslog file?

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/809#issuecomment-1985937189, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU6MWZZC6VYKRBPPLL3YXHNELAVCNFSM6AAAAABEMFH5USVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBVHEZTOMJYHE . You are receiving this because you authored the thread.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

fpusan commented 3 months ago

Can't see the syslog here, maybe you need to add .txt to the file name for github to accept it

laibinhuang commented 3 months ago

the version is: SqueezeMeta v1.6.3

I am rerunning it: -binners "maxbin, metabat, concoct" it doesn't work.

On Fri, Mar 8, 2024 at 10:37 AM Fernando Puente-Sánchez < @.***> wrote:

Can't see the syslog here, maybe you need to add .txt to the file name for github to accept it

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/809#issuecomment-1986023359, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU2OZCQZSFKEYDO65ADYXHSOHAVCNFSM6AAAAABEMFH5USVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWGAZDGMZVHE . You are receiving this because you authored the thread.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

fpusan commented 3 months ago

Yes, I understand. Can you share the syslog file inside the project's directory with me?

laibinhuang commented 3 months ago

I removed it for a new run: using Snakemake

I will get it to you once I have it

Thank you for your help! Laibin,

On Fri, Mar 8, 2024 at 10:47 AM Fernando Puente-Sánchez < @.***> wrote:

Yes, I understand. Can you share the syslog file inside the project's directory with me?

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/809#issuecomment-1986041840, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU5TNDOZTSENCTMV5GDYXHTSFAVCNFSM6AAAAABEMFH5USVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWGA2DCOBUGA . You are receiving this because you authored the thread.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

fpusan commented 3 months ago

Ok, great. Let us know

laibinhuang commented 3 months ago

The only issue here in the snakemake is out of memory, but when I am running in the without snakemake, it doesn't have problems.

below is the snakemake code: file_ids = glob_wildcards(WORKDIR+"resultstest/trim/{id}{read}.fastq{gz}")

rule SqueezeMeta: input: fastq=expand('resultstest/trim/{id}{read}.fastq.gz',id=file_ids.id, read=file_ids.read) output: SqM='results_test/{id}/results/21.{id}.stats' resources: runtime = 10000, mem_mb=102400 threads: 16 shell: ''' cp results_test/contigs/{wildcards.id}/{wildcards.id}.contigs.fa results_test/contigs/{wildcards.id}.fasta grep -w {wildcards.id} results_test/SqMeta.txt > results_test/{wildcards.id }.txt

to avoid error:

/home/lbhuang/mambaforge/envs/SqueezeMeta/etc/conda/activate.d/activate-binutils_linux-64.sh:

line 68: ADDR2LINE: unbound variable

/home/lbhuang/mambaforge/envs/SqueezeMeta/etc/conda/activate.d/activate-gcc_linux-64.sh:

line 110: SYS_SYSROOT: unbound variable

do

set +u source /home/lbhuang/mambaforge/envs/SqueezeMeta/etc/conda/activate.d/activate-binutils_linux-64.sh source /home/lbhuang/mambaforge/envs/SqueezeMeta/etc/conda/activate.d/activate-gcc_linux-64.sh source activate SqueezeMeta set -u rm -r results_test/{wildcards.id} #to avoid any error: folder exist; if you restart a previous project, then don't need this SqueezeMeta.pl -m coassembly -p results_test/{wildcards.id} -s results_test/{wildcards.id}.txt -f "results_test/trim" -extassembly "results_test/contigs/{wildcards.id}.fasta" --norename -binners "concoct,maxbin,metabat2" -c 1000 -b 20 sqm2zip.py /home/lbhuang/Moore/results_test/{wildcards.id} /home/lbhuang/Moore/results_test/ '''

rule all: input: expand('results_test/{id}/results/21.{id}.stats', id=file_ids.id)

On Fri, Mar 8, 2024 at 10:51 AM Fernando Puente-Sánchez < @.***> wrote:

Ok, great. Let us know

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/809#issuecomment-1986048106, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU7NPU7ND5UBPI4LXQ3YXHUBHAVCNFSM6AAAAABEMFH5USVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWGA2DQMJQGY . You are receiving this because you authored the thread.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

fpusan commented 3 months ago

So is the problem fixed now? Are metabat2 and concoct running?

laibinhuang commented 3 months ago

they stop at the taxonomy step due to memory issues; I am trying not to use Snakemake (do multiple samples together). I will let you know.

Thank you, Laibin

On Mon, Mar 11, 2024 at 10:55 AM Fernando Puente-Sánchez < @.***> wrote:

So is the problem fixed now? Are metabat2 and concoct running?

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/809#issuecomment-1988778193, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU2DANY5IXPV635M67TYXXHWVAVCNFSM6AAAAABEMFH5USVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBYG43TQMJZGM . You are receiving this because you authored the thread.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

fpusan commented 2 months ago

Closing due to lack of activity, feel free to reopen