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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Can't open /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta #802

Closed laibinhuang closed 2 months ago

laibinhuang commented 4 months ago

SqueezeMeta.pl -m coassembly -p /home/lbhuang/Moore/results_2021/CA2021 -s /home/lbhuang/Moore/results_2021/SqMeta.txt -f "/home/lbhuang/Moore/results_2021/trim" -extassembly "/home/lbhuang/Moore/results_2021/contig" -binners maxbin, metabat, concoct -c 1000

I get an issue with: Now creating directories Reading configuration from /home/lbhuang/Moore/results_2021/CA2021/SqueezeMeta_conf.pl [0 seconds]: STEP1 -> RUNNING ASSEMBLY: 01.run_all_assemblies.pl (megahit)  External assembly provided: /home/lbhuang/Moore/results_2021/contig/. Overriding assembly cp: -r not specified; omitting directory '/home/lbhuang/Moore/results_2021/contig/' Renaming contigs in /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta Can't open /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally 

laibinhuang commented 4 months ago

Dear Javier,

ANy suggestion for this parts, I provide my own contigs in a folder for this, but it doesn't work:

p: -r not specified; omitting directory '/home/lbhuang/Moore/results_2021/contig/' Renaming contigs in /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta Can't open /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta

laibinhuang commented 4 months ago

Meanwhile, How can I assign an output dir for the result, when I use -o, but it still create a new output-dir that different from mine.

Thank you

fpusan commented 4 months ago

Hi, answering here though I think this has also come up in a different issue. You need to specify a fasta file with --extassembly, not a directory The output directory is controlled with the -p parameter (unless you are using the sequential mode), the way you did it in your original post should be correct.

laibinhuang commented 4 months ago

Hi, if I need to do a sequential model using my contig for each sample, how can I incorporate extassembly flag?

since -extassembly can only have a fasta file, but I will have more than one fasta for the sequential model.

SqueezeMeta.pl -m sequential -s /home/lbhuang/Moore/results_2021/SqMeta.txt -f "/home/lbhuang/Moore/results_2021/trim" *-extassembly "/home/lbhuang/Moore/results_2021/contig/.fasta"** -binners maxbin, metabat, concoct -c 1000 -t 32

laibinhuang commented 4 months ago

thank you,

laibinhuang commented 4 months ago

Ok, thanks for the clarification.

On Tue, Mar 5, 2024 at 6:47 AM Fernando Puente-Sánchez < @.***> wrote:

Hi, answering here though I think this has also come up in a different issue. You need to specify a fasta file with --extassembly, not a directory The output directory is controlled with the -p parameter, the way you did it in your original post should be correct.

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/802#issuecomment-1978703416, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU6WWTQXYB7PPRHCQALYWW5E5AVCNFSM6AAAAABD6VCJQSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZYG4YDGNBRGY . 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