Reading gffs: Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : row names contain missing values
iferres opened this issue · 3 comments
Thankyou! I repulled/installed pagoo via devtools. there is progress but now i see this error
p <- panaroo_2_pagoo(gene_presence_absence_csv = gpa_csv, gffs = gffs)
Reading csv file (panaroo).
Processing csv file.
Removing 314 genes tagged as 'refound', 'stop', and/or 'length' by panaroo.
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/01_A1.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/02_B4.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/02_F4.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/03_C2.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/05_A8.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/33_A7.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/44MNt_B4_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/63VAs-B3_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/63VAs-Sm1_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/68VAs-B3_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/68VPs-B6_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/81UNt-Sm4_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/83VAs-Sm8_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/83VPs-KB5_GCF_007197715.1_ASM719771v1_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/87UNt-Sm4_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/88MNs-Sm2_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/88VPs-Sm9_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/90VAs-B6_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/90VAs-Sm9_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/9VPs-B5_contigs.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/ATCC-51524_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/Dp_81Mnt_Sm4.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1914_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1922_CDC39-95_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1931_CDC4294-98_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1933_CDC4545-98_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1934_CDC4709-98_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1937_CDC4199-99_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL1939_CDC4792-99_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3033_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3043_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3050_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3052_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3065_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3069_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3070_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3077_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3084_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3086_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3090_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3246_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3250_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3256_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3264_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3274_genomic.gff3
Reading gff file /lustre/groups/liu_price_lab/mlaziz/Dp/panaroo-020923-bakta/gff/KPL3911_genomic.gff3
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
row names contain missing values
Originally posted by @malihaaziz in #59 (comment)
Lets open a separate issue to tackle this.
Thankyou for creating a new ticket but you can close it now. I did a new install from you git and suddenly everything started working beautifully! no errors no warnings! Thankyou for addressing all the issues so quickly! it is a much needed tool!
You're welcome, please don't hesitate to report any other issue. Regards,
Ignacio