IOError: [Errno 2] No such file or directory

[jolespin]

Here's my command:

(ratt_env) -bash-4.1$ RATT-with-GFF/RATTwithGFF.py Gene_Models/spp.gff3 Gene_Models/spp.scaffolds.fa Assemblies/Sch523_scaffolds.fasta refToQuery Strain

<RATTwithGFF.py> checking for valid input files...

<RATTwithGFF.py> input files are valid
Traceback (most recent call last):
  File "RATT-with-GFF/RATTwithGFF.py", line 672, in <module>
    main()
  File "RATT-with-GFF/RATTwithGFF.py", line 35, in main
    gffFileName = fixLineEndings(gffFileName)
  File "RATT-with-GFF/RATTwithGFF.py", line 108, in fixLineEndings
    with open(newFileName,"wb") as outFile:
IOError: [Errno 2] No such file or directory: 'temp_Gene_Models/spp.gff3'

Here's the version:

#!/usr/bin/env python2.7

##############################################################################################################
# RATTwithGFF.py                                                                                             #
# Author: Preston Basting                                                                                    #
# Last Changed 06/21/18                                                                                      #
# Contact: pjb68507@uga.edu                                                                                  #
# Function: This program is designed to run the rapid annotation transfer tool (RATT) using gff as input.    #
#   RATT is a tool for transferrin annotations from one genome to another. Normally, RATT requires embl as   #
#   the annotation format. This program uses other scripts to handle the file conversions and corrects for   #
#   the errors that often occur. Produces  gff files as output.                                              #
##############################################################################################################

[jolespin]

Figured it out. The way you coded this means that these files need to be in the same current working directory.

[jolespin]

Here is the error now:

<RATTwithGFF.py> converting contig01_circ.gff to contig01_circ.embl....
usage: EMBLmyGFF3 [-h] [-a] [-c CREATED]
                  [-d {CON,PAT,EST,GSS,HTC,HTG,MGA,WGS,TSA,STS,STD}]
                  [-g ORGANELLE] [-i LOCUS_TAG] [-k KEYWORD [KEYWORD ...]]
                  [-l CLASSIFICATION]
                  [-m {genomic DNA,genomic RNA,mRNA,tRNA,rRNA,other RNA,other DNA,transcribed RNA,viral cRNA,unassigned DNA,unassigned RNA}]
                  [-o OUTPUT] [-p PROJECT_ID] [-q]
                  [-r {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}]
                  [-s SPECIES] [-t {linear,circular}] [-v]
                  [-x {PHG,ENV,FUN,HUM,INV,MAM,VRT,MUS,PLN,PRO,ROD,SYN,TGN,UNC,VRL}]
                  [-z] [--ah {One of the parameters above}] [--de DE]
                  [--ra RA [RA ...]] [--rc RC] [--rg RG] [--rl RL] [--rt RT]
                  [--rx RX] [--email EMAIL] [--expose_translations]
                  [--force_unknown_features] [--force_uncomplete_features]
                  [--interleave_genes] [--keep_duplicates]
                  [--locus_numbering_start LOCUS_NUMBERING_START]
                  [--no_progress] [--no_wrap_qualifier] [--shame]
                  [--translate]
                  [--use_attribute_value_as_locus_tag USE_ATTRIBUTE_VALUE_AS_LOCUS_TAG]
                  [--uncompressed_log] [--version VERSION] [--strain STRAIN]
                  [--environmental_sample]
                  [--isolation_source ISOLATION_SOURCE] [--isolate ISOLATE]
                  gff_file fasta
EMBLmyGFF3: error: unrecognized arguments: contig_fasta/contig01_circ.fa

fixing line-breaks for: contig01_circ.embl....
Traceback (most recent call last):
  File "RATT-with-GFF/RATTwithGFF.py", line 673, in <module>
    main()
  File "RATT-with-GFF/RATTwithGFF.py", line 48, in main
    gffsToEmbls(contigs)
  File "RATT-with-GFF/RATTwithGFF.py", line 201, in gffsToEmbls
    cleanEmbl(contig)
  File "RATT-with-GFF/RATTwithGFF.py", line 257, in cleanEmbl
    cleanEmblLines = fixBrokenLines(embl)
  File "RATT-with-GFF/RATTwithGFF.py", line 241, in fixBrokenLines
    with open(fileName) as file:
IOError: [Errno 2] No such file or directory: 'contig_embl/contig01_circ_tmp1.embl'

[luciaalvarez95]

Hi! I have exactly the same problem, did you find a solution?

Many thanks

[jolespin]

Is this supposed to convert genbank to gff? I think I ended up just using BioPython to parse the records and then format it for gff.

[luciaalvarez95]

Thanks for you reply! This pipeline should convert gff to embl, so then you can use that embl as an input for RATT. I have been struggling for a while to run that program correctly because I am not able to get a correct conversion from gff to embl and this doesn't seem to work either.

[jolespin]

Author hasn't touched this repository in 2 years so it might be good to look into another tool. I was looking into annotation transfer in the past and its a messy business.