Closed AMChalkie closed 4 years ago
When running run_sgrna_quant(FASTA, df_design, sg2gene) I see this comment: 4 sgRNA sequences were repetitive and will be discarded.
Final Mappability: 88.2023%
Parsed with column specification:
cols(
PZP_1 = col_character(),
PZP = col_character()
)
Error: by
can't contain join column id
which is missing from LHS
Run rlang::last_error()
to see where the error occurred.
rlang::last_error() <error/rlang_error>
by
can't contain join columnid
which is missing from LHS Backtrace:
- CB2::run_sgrna_quant(...)
- dplyr:::left_join.tbl_df(df_map, df_count, by = "id")
- dplyr:::common_by.character(by, x, y)
- dplyr:::common_by.list(by, x, y)
- dplyr:::bad_args(...)
- dplyr:::glubort(fmt_args(args), ..., .envir = .envir) Run
rlang::last_trace()
to see the full context.
When running: (with duplicates) run_sgrna_quant(FASTA, df_design)
run_sgrna_quant(FASTA, df_design)
I get Error in data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) : arguments imply differing number of rows: 79633, 79637
traceback() 3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA) 2: data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) 1: run_sgrna_quant(LIBRARY_FASTA, df_design)
Hi, can you share your fasta file?
Thank you,
Hyun-Hwan Jeong
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From: Alistair Chalk notifications@github.com Sent: Tuesday, November 26, 2019 7:54:08 PM To: LiuzLab/CB2 CB2@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [LiuzLab/CB2] run_sgrna_quant fails (#3)
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When running run_sgrna_quant(FASTA, df_design, sg2gene) I see this comment: 4 sgRNA sequences were repetitive and will be discarded.
Final Mappability: 88.2023% Parsed with column specification: cols( PZP_1 = col_character(), PZP = col_character() ) Error: by can't contain join column id which is missing from LHS Run rlang::last_error() to see where the error occurred.
rlang::last_error() <error/rlang_error> by can't contain join column id which is missing from LHS Backtrace:
When running: (with duplicates) run_sgrna_quant(FASTA, df_design)
run_sgrna_quant(FASTA, df_design)
I get Error in data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) : arguments imply differing number of rows: 79633, 79637
traceback() 3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA) 2: data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) 1: run_sgrna_quant(LIBRARY_FASTA, df_design)
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Here you go: broadgpp_brie_crispr_library.fasta.gz
Hi,
I see the following error:
Error in data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) : arguments imply differing number of rows: 79633, 79637
Suggest adding a more robust check in the output section. Cheers Alistair