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pbasting / RATT-with-GFF

RATT-with-GFF enables Rapid Annotation Transfer Tool (RATT) to be used with a GFF as your annotation file. RATT is a great tool for transferring annotations from one genome to another, but requires the annotations be in EMBL format. This pipeline is designed to use existing file conversion tools in order to run RATT with GFF annotations files
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error: unrecognized arguments: chromosome_1 #3

Open elcortegano opened 4 years ago

elcortegano commented 4 years ago

I got the following error when running RATTwithGFF:

converting chromosome_1.gff to chromosome_1.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: chromosome_1 fixing line-breaks for: chromosome_1.embl.... Traceback (most recent call last): File "./RATTwithGFF.py", line 672, in main() File "./RATTwithGFF.py", line 48, in main gffsToEmbls(contigs) File "./RATTwithGFF.py", line 200, in gffsToEmbls cleanEmbl(contig) File "./RATTwithGFF.py", line 256, in cleanEmbl cleanEmblLines = fixBrokenLines(embl) File "./RATTwithGFF.py", line 240, in fixBrokenLines with open(fileName) as file: IOError: [Errno 2] No such file or directory: 'contig_embl/chromosome_1_tmp1.embl'

I have traced the error to the -a (--accession) option of EMBLmyGFF3, which is passed with the value "contig" (eg. it can be "chromosome_1"), but according to EMBLmyGFF3 it should be a boolean.

If this option is removed, EMBLmyGFF3 runs and the script continues. However, I am still not confident that this is the expected behaviour in RATT-with-GFF. What should be the value of the a option? is it necessary in the pipeline?

Thank you

chemy-cm commented 3 years ago

I have the name error with you. and I have test the example of this script，I got the same error. So I think this script have problem,we need to change the -a contig options