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flass / pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
GNU General Public License v3.0
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Usage: errors when using pantagruel command with TASKS #5

Closed ElitaJaun closed 5 years ago

ElitaJaun commented 5 years ago

Hi Florent,

I got the following error when running command pantagruel -i /environ_pantagruel_databasename.sh fetch

This is Pantagruel pipeline version 02fa4e538118cb231a3f843d57b21685db538777 using source code from repository '/home/elita/pantagruel_pipeline/pantagruel'

will run tasks: 0

[2019-03-05 16:27:19] Pantagrel pipeline step 0: fetch public genome data from NCBI sequence databases and annotate private genomes. did not find the relevant taxonomy flat files in '/home/elita/NCBI/Taxonomy_2019-03-05/'; download the from NCBI Taxonomy FTP cd ok, cwd=/pub/taxonomy
55885994 bytes transferred in 10 seconds (5.30 MiB/s)
Total 6 files transferred taxcat.tar.gz: OK taxdump.tar.gz: OK /home/elita extract assembly data from folder '/home/elita/gbs_ncbi' /home/elita/pantagruel_pipeline/pantagruel/scripts/pipeline/pantagruel_pipeline_00_fetch_data.sh: line 264: /home/elita/databasename/00.input_data/genome_infos/assemblies_list: No such file or directory Traceback (most recent call last): File "/home/elita/pantagruel_pipeline/pantagruel/scripts/check_create_cds_from_genomic.py", line 22, in with open(nfldirassemb, 'r') as fldirassemb: IOError: [Errno 2] No such file or directory: '/home/elita/databasename/00.input_data/genome_infos/assemblies_list' /home/elita/pantagruel_pipeline/pantagruel/scripts/pipeline/pantagruel_pipeline_00_fetch_data.sh: line 288: /home/elita/pantagruel_pipeline/pantagruel/scripts/groom_refseq_data.sh/home/elita/databasename/00.input_data/assemblies: Not a directory Traceback (most recent call last): File "/home/elita/pantagruel_pipeline/pantagruel/scripts/extract_metadata_from_gbff.py", line 77, in with open(nfldirassemb, 'r') as fldirassemb: IOError: [Errno 2] No such file or directory: '/home/elita/databasename/00.input_data/genome_infos/assemblies_list' ERROR:

Any advise? Thanks.

bw, Elita

flass commented 5 years ago

Hi Elita, well spotted! it's due to a change I had just introduced. it si fixed in commits 6cef840, 843ba27 and dd65fb2.