Ge94
commented
8 months ago Hi Junhui, thank you for your interest in this repo! I tried querying ENA API with the sample accession associated with SRR26115692 (SRS18928889), but unfortunately the output is also empty. For reference:
curl -X POST -H "Content-Type: application/x-www-form-urlencoded" -d 'result=sample&query=secondary_sample_accession=%22SRS18928889%22&fields=all&format=tsv' "https://www.ebi.ac.uk/ena/portal/api/search"
I see that these samples have recently been uploaded to ENA. It usually takes around a week for ENA to index submitted files (despite them appearing on the ENA browser!), and this timespan might temporarily increase depending on eventual backlogs. I would suggest to retry in the next days. A persisting error might suggest an issue during ENA's indexing processing, for which case it would be better for you to contact ENA support to identify the right procedure to follow.
junhuili
I tried to upload some MAGs, and it works for most of the bins (eg https://www.ebi.ac.uk/ena/browser/view/ERZ21824814), except for the bins from the metagenomes that were deposited on 2023-09-20. The error seems associated with "retrieve sample accession", but the metagenomes are available in ENA, eg https://www.ebi.ac.uk/ena/browser/view/SRR26115692.
Error: "Retrieving data for MAG submission... Retrieving info for genomes to submit... Retrieving project and run info from ENA (this might take a while)... Traceback (most recent call last): File "genome_upload.py", line 1274, in
file_generator()
File "genome_upload.py", line 1196, in file_generator
genomes = ENA_uploader.create_genome_dictionary(samples_xml)
File "genome_upload.py", line 1267, in create_genome_dictionary
extract_ENA_info(genomeInfo, self.upload_dir, self.username, self.password)
File "genome_upload.py", line 748, in extract_ENA_info
sampleInfo = get_sample(sampleAccession, webin, password)
File "genome_upload.py", line 684, in get_sample
return json.loads(response.text)[0]
IndexError: list index out of range"
Table: Checklist_ENA-bin0.csv