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BiG-MAP.download.py can't download test-set: ftp site is decommissioned #2

Open edissepo opened 4 years ago

edissepo commented 4 years ago

Upon trying to download the test project as provided in the readme, an error occurs claiming that the site cannot be accessed (No such directory ‘sra/sra-instant/reads/ByRun/sra/SRR/SRR013/SRR013549’.) - see below for full error code. Trying manually with wget gives the same error. Found online an explanation (https://ncbiinsights.ncbi.nlm.nih.gov/2019/10/17/users-of-the-sra-ftp-site-try-the-sra-toolkit/) - the ncbi ftp site is decommissioned since December 2019.

Solve: Try incorporating the SRA-tool in BiG-MAP.download.py

Good luck.

Error: Namespace(acclist='../SRR_Acc_List.txt', outdir='../../scratch/') --2020-10-19 12:24:37-- ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR013/SRR013549/SRR013549.sra => ‘../../scratch/SRR013549.sra’ Resolving ftp-trace.ncbi.nih.gov (ftp-trace.ncbi.nih.gov)... 130.14.250.11, 2607:f220:41e:250::10, 2607:f220:41e:250::13, ... Connecting to ftp-trace.ncbi.nih.gov (ftp-trace.ncbi.nih.gov)|130.14.250.11|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /sra/sra-instant/reads/ByRun/sra/SRR/SRR013/SRR013549 ... No such directory ‘sra/sra-instant/reads/ByRun/sra/SRR/SRR013/SRR013549’.

Traceback (most recent call last): File "BiG-MAP.download.py", line 194, in main() File "BiG-MAP.download.py", line 188, in main downloadSRA(acc, args.outdir) File "BiG-MAP.download.py", line 127, in downloadSRA res_download = subprocess.check_output(cmd_download, shell=True) File "/opt/miniconda3/lib/python3.6/subprocess.py", line 356, in check_output **kwargs).stdout File "/opt/miniconda3/lib/python3.6/subprocess.py", line 438, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command 'wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR013/SRR013549/SRR013549.sra -P ../../scratch/' returned non-zero exit status 8.

victoriapascal commented 3 years ago

I have just done a test with the data and command from the tutorial and I can't reproduce your error. Did you activate the BiG-MAP_process environment? What command did you use exactly? Do you have permission to create a new folders?