laibinhuang

name of input errors:

2

I run this in snakemake; and get the name of input errors: for other code in this snakemeke file, I don't have the errors please help file_ids = glob_wildcards(WORKDIR+"data/Metagenomics_test/{id}_R{read}.fastq{gz}") ##setup...

python3.10/subprocess.py", line 524, in run raise calledprocesserror

4

when I run snakemake, I got this bug: please help [Wed Aug 24 09:29:59 2022] rule fastqc_raw: input: data/Metagenomic2020/P92_R2.fastq.gz output: results/report/fastqc/raw/P92_R2_fastqc.html jobid: 3 reason: Missing output files: results/report/fastqc/raw/P92_R2_fastqc.html wildcards: id=P92,...

-binners, just do maxbin

11

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,

Can't open /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta

6

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...

Kraken2 classification errors

1

I am using Kraken2 for classification, but I get some errors: would you mind helping me out. Thank you very much. The code:KRAKEN_DB="/home/lbhuang/ref/kraken/ABFPV/"  #note ABFPV is a database built using...

Hi Diting team, I get **pathways_relative_abundance_gene_level.tab**, it doesn't produce **pathways_relative_abundance.tab** due to so many samples Can I use some script (pathway.py in the scripts) to produce the **pathways_relative_abundance.tab** Thank you,...

Error for visualize the abundance table using my own combination of samples

1

Dear Xue, thank you for your program here, I would like to discuss a recent issue I have met: I group my samples in **pathways_relative_abundance.tab,** but it produces the error...

ERROR sequence/io/sequence_lib.cpp : 70 - PE library number of reads is odd: 49891647!'

1

Dear When I run Diting, /home/lbhuang/miniconda3/envs/diting-env/bin/diting.py -r /home/lbhuang/Moore/data/Metagenomics_test/ -o /home/lbhuang/Moore/results_test/Diting_result/ I get this erorr: 2022-09-23 20:27:50 - MEGAHIT v1.2.9 2022-09-23 20:27:50 - Using megahit_core with POPCNT and BMI2 support 2022-09-23...

I am little bit confused, what do you mean by having the dependencies installed and added to the $path, can you take one for example: like I have bbmap in...