SRR upload error seen in workflow
Most organisms require multiple SRR accessions to accurately analyze the assembly data. The pipeline was run as dictated in the protocol with the stated parameters but threw the following error message pertaining to gathering the SRR data from NCBI and creating a hiveseq object with the data:
Next step is to try using the api to add multiple SRA files and adjust the existing script to include the parameters necessary. Code snippets for template below.
def apiLogin():
global cookies
user = input("\nEnter your username on " + hiveVal + " (email address): ")
password = getpass.getpass()
loginParams = {'api': '0', 'cmdr': 'login', 'login': user, 'pswd': password}
response = requests.get(basename, params=loginParams)
if response.text != '':
print(response.text)
apiLogin() # Try again
else:
cookies = response.cookies
apiLogin()
Correct SRR parameters:
lst=[]
strIDs = ','.join(str(v) for v in lst)
SRRParams = {'cmdr': 'propget', 'prop': 'id,_brief', 'mode': 'csv', 'ids': strIDs, 'raw': '1'}
responseSRR = requests.get(basename, SRRParams, cookies=cookies)
decoded_content = responseSRR.content.decode('utf-8')
cr = csv.reader(decoded_content.splitlines(), delimiter=',')
with open('TEMPIDFile.csv', 'w+', newline='') as IDFile:
my_list = list(cr)
for row in my_list:
print(row[3].split()[0], file=IDFile)
Alternatively, use the API to read the SRR files into HIVE3. Go to the webpage GUI and run the pipeline with the newly added SRR files by selecting them in the "HIVE reads" field instead of entering the SRA information in "SRR accessions".
SRR upload error seen in workflow
Most organisms require multiple SRR accessions to accurately analyze the assembly data. The pipeline was run as dictated in the protocol with the stated parameters but threw the following error message pertaining to gathering the SRR data from NCBI and creating a hiveseq object with the data:
Next step is to try using the api to add multiple SRA files and adjust the existing script to include the parameters necessary. Code snippets for template below.
Correct SRR parameters:
Alternatively, use the API to read the SRR files into HIVE3. Go to the webpage GUI and run the pipeline with the newly added SRR files by selecting them in the "HIVE reads" field instead of entering the SRA information in "SRR accessions".