Grabseqs error about grabseqs HOT 9 OPEN

metadata = requests.get("https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/runinfo?acc="+pacc) 

seems work

from grabseqs.

Thank you chansigit, it is working again

from grabseqs.

same

from grabseqs.

same problem than Nov 2022:

(grabseqs) ant@hillary:/LemonSharkGSS$ grabseqs sra SRR23340818 -t 12
Traceback (most recent call last):
File "/home/ant/miniconda3/envs/grabseqs/bin/grabseqs", line 11, in
sys.exit(main())
File "/home/ant/miniconda3/envs/grabseqs/lib/python3.7/site-packages/grabseqslib/init.py", line 58, in main
metadata_agg = process_sra(args, zip_func)
File "/home/ant/miniconda3/envs/grabseqs/lib/python3.7/site-packages/grabseqslib/sra.py", line 31, in process_sra
metadata_agg)
File "/home/ant/miniconda3/envs/grabseqs/lib/python3.7/site-packages/grabseqslib/sra.py", line 97, in get_sra_acc_metadata
run_col = lines[0].index("Run")
ValueError: 'Run' is not in list
(grabseqs) ant@hillary:/LemonSharkGSS$

At that time, I followed your (below) suggestion and it went back to work:
Try replacing /usr/local/lib/python3.6/site-packages/grabseqslib/sra.py line 94 with
metadata = requests.get("https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/sra-db-be.cgi?rettype=runinfo&term="+pacc)

Any new suggestion? Thank you!

from grabseqs.

It didn't work.

from grabseqs.

sra.txt
rename this txt with sra.py and copy it to /yourpathto/grabseqslib/. replacing the former one will solve the problem for now. It is caused by the replacement of trace.ncbi I suppose. If it doesn't work again, just check whether the path https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be is still working and find a new one.

from grabseqs.

doesn't work again

from grabseqs.

if someone is facing this issue now, then try replacing
/usr/local/lib/python3.6/site-packages/grabseqslib/sra.py line 45 with
metadata = requests.get("https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/sra-db-be.cgi?rettype=runinfo&term="+pacc)

from grabseqs.