sjdlabgroup / SAHMI

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run extract_microbiome_reads.r and Error in split.default(taxid, ceiling(seq_along(taxid)/opt$ntaxid)) #19

Open sheyong111 opened 5 months ago

sheyong111 commented 5 months ago

Rscript /data3/shey/Data/HNSC/SAHMI-main/SAHMI-main/functions/extract_microbiome_reads.r \ --sample_name SRR16936931 \ --fq SRR16936931/SRR16936931_1.fq \ --fq SRR16936931/SRR16936931_2.fq \ --kraken_report SRR16936931/SRR16936931.kraken.report.txt \ --mpa_report SRR16936931/SRR16936931.kraken.report.mpa.txt \ --out_path SRR16936931/extract_microbiome_reads ── Attaching core tidyverse packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.4 ✔ forcats 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 ✔ purrr 1.0.2
── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() ℹ Use the conflicted package (http://conflicted.r-lib.org/) to force all conflicts to become errors [conflicted] Will prefer dplyr::filter over any other package. [conflicted] Will prefer dplyr::lag over any other package. Error in split.default(taxid, ceiling(seq_along(taxid)/opt$ntaxid)) : first argument must be a vector Calls: split -> split.default Execution halted