Hi, I’m trying to download a sample bam file from EGA with icgc-get with docker container enabled.
The command line I’m using is:
./icgc-get -d True download FI9995
The download process fails. In spite of the fact that it is reported an error with a missing directory at the end, seems like the problem starts with a time out occurred during downloading. Multiple executions of the previous command end up with the same result. Below I copy part of the content of the log file:
| Output: Ticket: 4f57ed6a-d4d2-4c1b-82fe-572b3ffd03af
| URL: http://ega.ebi.ac.uk/ega/rest/ds/v2/downloads/4f57ed6a-d4d2-4c1b-82fe-572b3ffd03af
| Establishing Data Stream for: 4f57ed6a-d4d2-4c1b-82fe-572b3ffd03af
| Data Stream for 4f57ed6a-d4d2-4c1b-82fe-572b3ffd03af is established
| Path: /icgc/mnt/_EGAZ00001225589_efcf90ee-53ae-4f9f-b29a-e0a83ca70272_f5c9381090a53c54358feb2ba5b7a3d7.bam.cip
| Starting transfer loop for 4f57ed6a-d4d2-4c1b-82fe-572b3ffd03af (true)
| Download Error occurred at Stage 4
| Error: Read timed out
| Completed download: /EGAZ00001225589/efcf90ee-53ae-4f9f-b29a-e0a83ca70272
/f5c9381090a53c54358feb2ba5b7a3d7.bam.cip: false (0/1) | Download Failed: /EGAZ00001225589/efcf90ee-53ae-4f9f-b29a-e0a83ca70272/f5c9381090a53c54358feb2ba5b7a3d7.bam.cip 4f57ed6a-d4d2-4c1b-82fe-572b3ffd03af
| Iteration Done! (0 / 1)
| Download Attempt Completed. 1 of 1 tickets downloaded successfully.
| Post-Download: No outstanding Tickets
| Download Iteration Completed. Retry loop for 0 unsuccessful downloads.
Traceback (most recent call last):
File "icgcget/cli.py", line 397, in
File "icgcget/cli.py", line 393, in main
File "site-packages/click/core.py", line 722, in __call__
File "site-packages/click/core.py", line 697, in main
File "site-packages/click/core.py", line 1066, in invoke
File "site-packages/click/core.py", line 895, in invoke
File "site-packages/click/core.py", line 535, in invoke
File "site-packages/click/decorators.py", line 17, in new_func
File "icgcget/cli.py", line 261, in download
File "icgcget/commands/download.py", line 130, in download
File "icgcget/commands/download.py", line 201, in client_download
File "icgcget/clients/ega/ega_client.py", line 99, in download
OSError: [Errno 2] No such file or directory: '/icgc/mnt'
Failed to execute script cli
Could you please help me to troubleshoot the problem?