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louiejtaylor / grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
MIT License
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Grabseqs error #56

Open xsq2022 opened 1 year ago

xsq2022 commented 1 year ago

Hi, I met this problem when I used grabseqs. image Traceback (most recent call last): File "/media/home/user05/anaconda3/envs/python36/bin/grabseqs", line 11, in sys.exit(main()) File "/media/home/user05/anaconda3/envs/python36/lib/python3.6/site-packages/grabseqslib/init.py", line 58, in main acclist, metadata_agg = get_sra_acc_metadata(sra_identifier, args.outdir, args.list, not args.SRR_parsing, metadata_agg) File "/media/home/user05/anaconda3/envs/python36/lib/python3.6/site-packages/grabseqslib/sra.py", line 52, in get_sra_acc_metadata run_col = lines[0].index("Run") ValueError: 'Run' is not in list Could you please tell me how to solve this problem? Thanks.

deyuanyang commented 1 year ago

same

AntonioBaeza commented 1 year ago

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!

xsq2022 commented 1 year ago

It didn't work.

LeeYEAH2 commented 1 year ago

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.

chansigit commented 1 year ago

doesn't work again

chansigit commented 1 year ago 
metadata = requests.get("https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/runinfo?acc="+pacc)

seems work

AntonioBaeza commented 1 year ago

Thank you chansigit, it is working again

ufaroooq commented 1 year ago

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)

swelbo commented 7 months ago

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)

Worked for me thank you