-binners, just do maxbin #809
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Enclose the binners between quotes, that is: |
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Just in case, what version of SqueezeMeta are you using and can you provide your syslog file? |
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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?
—
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--
*-----------------------------------------------------------*
*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
*************************************************
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Can't see the syslog here, maybe you need to add |
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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
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--
*-----------------------------------------------------------*
*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
*************************************************
|
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Yes, I understand. |
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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?
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--
*-----------------------------------------------------------*
*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
*************************************************
|
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Ok, great. Let us know |
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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+"results_test/trim/{id}_{read}.fastq{gz}")
rule SqueezeMeta:
input:
fastq=expand('results_test/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
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--
*-----------------------------------------------------------*
*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
*************************************************
|
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So is the problem fixed now? Are metabat2 and concoct running? |
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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?
—
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<#809 (comment)>,
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.
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
*************************************************
|
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Closing due to lack of activity, feel free to reopen |
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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,
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