Closed raw937 closed 9 hours ago
Hi Rick,
If this is exactly how your GFF file appears:
gff-version 3
Sequence Data: seqnum=1;seqlen=499946;seqhdr="ATCC_phageG"
Model Data: version=pyrodigal.v3.5.2;run_type=Metagenomic;model="59|Gut_phage_code_11c|V|29.9|11|1";gc_cont=29.95;transl_table=11;uses_sd=1
phageY pyrodigal_v3.5.2 CDS 407 610 21.2 + 0 ID=1;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 987 1292 36.5 + 0 ID=2;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 1555 1833 36.1 + 0 ID=3;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 1939 2334 50.7 + 0 ID=4;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 2443 2628 19.5 + 0 ID=5;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 2640 2921 26.0 + 0 ID=6;Name=hypothetical;Alias=phrog_15464;Dbxref=PHROG;evalue=3.8e-39;product_start=4;produ
ct_end=93;product_length=89
Then I suspect that the parsing issue is with the header rows not being 'commented-out', i.e. they should start with a #
:
#gff-version 3
#Sequence Data: seqnum=1;seqlen=499946;seqhdr="ATCC_phageG"
#Model Data: #version=pyrodigal.v3.5.2;run_type=Metagenomic;model="59|Gut_phage_code_11c|V|29.9|11|1";gc_cont=29.95;transl_table=11;uses_sd=1
phageY pyrodigal_v3.5.2 CDS 407 610 21.2 + 0 ID=1;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 987 1292 36.5 + 0 ID=2;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 1555 1833 36.1 + 0 ID=3;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 1939 2334 50.7 + 0 ID=4;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 2443 2628 19.5 + 0 ID=5;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 2640 2921 26.0 + 0 ID=6;Name=hypothetical;Alias=phrog_15464;Dbxref=PHROG;evalue=3.8e-39;product_start=4;produ
ct_end=93;product_length=89
Let me know if this fixes your issue!
Nope. The headers look fine
##gff-version 3
# Sequence Data: seqnum=1;seqlen=499946;seqhdr="phageY"
# Model Data: version=pyrodigal.v3.5.2;run_type=Metagenomic;model="59|Gut_phage_code_11c|V|29.9|11|1";gc_cont=29.95;transl_table=11;uses_sd=1
phageY pyrodigal_v3.5.2 CDS 407 610 21.2 + 0 ID=phageY_1;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 987 1292 36.5 + 0 ID=phageY_2;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length=
phageY pyrodigal_v3.5.2 CDS 1555 1833 36.1 + 0
Thoughts?
; error in starting gff. Look at [padlocbio/padloc] error in 'mutate()' (Issue #42).
Warning messages: 1: package ‘tidyverse’ was built under R version 4.3.3 2: package ‘ggplot2’ was built under R version 4.3.3 3: package ‘tibble’ was built under R version 4.3.3 4: package ‘tidyr’ was built under R version 4.3.3 5: package ‘readr’ was built under R version 4.3.3 6: package ‘purrr’ was built under R version 4.3.3 7: package ‘dplyr’ was built under R version 4.3.3 8: package ‘stringr’ was built under R version 4.3.3 9: package ‘forcats’ was built under R version 4.3.3 10: package ‘lubridate’ was built under R version 4.3.3 Warning message: One or more parsing issues, call
problems()
on your data frame for details, e.g.: dat <- vroom(...) problems(dat) Error inseparate_wider_delim()
: ! Expected 2 pieces in each element ofattributes
. ! 1 value was too short. ℹ Usetoo_few = "debug"
to diagnose the problem. ℹ Usetoo_few = "align_start"/"align_end"
to silence this message. Backtrace:[15:52:34] ERROR >> errexit on line 425
I think it's the GFF ? Thoughts?
Lines of the GFF gff-version 3 Sequence Data: seqnum=1;seqlen=499946;seqhdr="phageY" Model Data: version=pyrodigal.v3.5.2;run_type=Metagenomic;model="59|Gut_phage_code_11c|V|29.9|11|1";gc_cont=29.95;transl_table=11;uses_sd=1 phageY pyrodigal_v3.5.2 CDS 407 610 21.2 + 0 ID=1;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length= phageY pyrodigal_v3.5.2 CDS 987 1292 36.5 + 0 ID=2;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length= phageY pyrodigal_v3.5.2 CDS 1555 1833 36.1 + 0 ID=3;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length= phageY pyrodigal_v3.5.2 CDS 1939 2334 50.7 + 0 ID=4;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length= phageY pyrodigal_v3.5.2 CDS 2443 2628 19.5 + 0 ID=5;Name=Hypothetical;Alias=;Dbxref=;evalue=;product_start=;product_end=;product_length= phageY pyrodigal_v3.5.2 CDS 2640 2921 26.0 + 0 ID=6;Name=hypothetical;Alias=phrog_15464;Dbxref=PHROG;evalue=3.8e-39;product_start=4;produ ct_end=93;product_length=89
many thanks, Rick