MetaCompass

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Hi, was running the tutorial example: ``` $ python3 go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -1 tutorial/thao2000.1.fq -2 tutorial/thao2000.2.fq -l 150 -o tutorial/example1_output -t 30 --notimestamps ``` but it failed: ``` REFERENCE genome...

lxsteiner

snakemake: error: argument **-T/--restart-times: expected one argument**

3

hello i found this error when running metacompass please help me to understand what is that error mean and how to solve it usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache...

esraagithub

Could not open reference sequences file /refseq/markers/genome2markers.length

1

I ran the example `go_metacompass.py -1 SRS044742/SRS044742.denovo_duplicates_marked.trimmed.1.fastq -2 SRS044742/SRS044742.denovo_duplicates_marked.trimmed.2.fastq -U SRS044742/SRS044742.denovo_duplicates_marked.trimmed.singleton.fastq -l 100 -o example_output -k` It failed in the `reference_selection` step. When I checked the log, I found this...

zhan4429

snakemake: error: unrecognized arguments: -T

5

### COMMAND ### python3 go_metacompass.py -1 test_for.fastq -2 test_rev.fastq -l 250 -o MC_assembly -m 2 -t 10 -y 100 --clobber ###OUTPUT### MetaCompass metagenome assembler version 2.0.0 by Victoria Cepeda ([email protected])...

TealFurnholm

Error --pilon polish contigs

1

Hello, i am running the following command: #!/bin/bash #SBATCH -J metacom_CJ_Car #SBATCH -t UNLIMITED #SBATCH -p Node2 #SBATCH -n 12 python3 /home/geonho/tools/MetaCompass-2.0-beta/go_metacompass.py -r /home/geonho/WGS/REF_ACP/REF_GENOMES/C_rudii_JRPAMB4_complete_genome_NZ_CP041245/ACP_C_rudii.ref.fas -1 /home/geonho/WGS/trimmed/CJ_S7_L003_R1_001.fastq.gz -2 /home/geonho/WGS/trimmed/CJ_S7_L003_R2_001.fastq.gz -o /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ...

GeonhoCho

Error when running MetaCompass

1

Hi, I am running the following command: python3 go_metacompass.py -r NC_040570.1.fasta -1 ERR2040215_1fp.fq -2 ERR2040215_2fp.fq -t 10 And I get the following error: [Tue Mar 8 10:02:21 2022] Job 7:...

bgmfddg

Error in job reference_selection

2

Hi, I'm using MetaCompass v2.0-beta. Example1 worked but example2 didn't. It ended up with Error in job reference_selection while creating output files example2_output/reference_selection/mc.refseq.fna, example2_output/reference_selection/mc.refseq.ids. MissingOutputException in line 64 of /home/mpg02/MMTM/yiming.shi/metacompass/snakemake/metacompass.py:...

AKBode

I got the following Bowtie2 error: Error in rule bowtie2_map: jobid: 8 output: ctrl_mc/assembly/mc.index, ctrl_mc/assembly/mc.index, ctrl_mc/assembly/mc.sam, ctrl_mc/logs/bowtie2map.log shell: bowtie2-build -o 3 --threads 18 -q ctrl_mc/reference_selection/mc.refseq.fna ctrl_mc/assembly/mc.index 1>> ctrl_mc/assembly/mc.index 2>&1;bowtie2 -a...

mredrejo

Hi, I got some errors generated during installation on Catalina MacOS 10.15.7, related with _cstdaling_ library. I'm copying the output below. Any ideas?? Thanks In file included from ./src/utils/breadth.cpp:2: ./src/utils/stdc++.h:55:10:...

mredrejo

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

19

Hi, what does this mean? is it that the quality of my reads are bad or that I don't have any MAG related to the ref genome I am searching...

MarcelaHer