I am receiving errors listed below when I run fasterq-dump on sra files that were downloaded earlier using prefetch. Fasterq-dump is run with default settings, the only command line arguments being used are -p, -O and -t. The input data consists of relatively large files, but there is enough RAM and disk space. The errors are reported at the beginning of the join phase, which then proceeds as if nothing has happened. However I am not sure about the impact of these errors on the output data. Errors occur for approximately half of sra files. Very occasionally an additional error will be thrown after join phase processing has already started (see second example, error at 0.27% progress).
This problem is similar to issue #331, but I am reporting it against a newer version of sra-tools. Unfortunately, issue #331 does not offer any insights on the nature of the error, nor any workarounds.
Help will be greatly appreciated.
SRR12599535
lookup :|-------------------------------------------------- 100%
merge : 14446522576
join :| 0.00%2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 2591896 of 3086968
2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1035800 of 3086968
2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1554488 of 3086968
2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 2073192 of 3086968
-------------------------------------------------- 100%
concat :|-------------------------------------------------- 100%
spots read : 1,945,116,998
reads read : 3,890,233,996
reads written : 3,890,233,996
SRR12599536
lookup :|-------------------------------------------------- 100%
merge : 15131824452
join :| 0.00%2022-11-05T22:56:02 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 2419416 of 2881016
2022-11-05T22:56:02 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1935208 of 2881016
2022-11-05T22:56:02 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1451000 of 2881016
0.27%2022-11-05T22:56:15 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 969080 of 2881016
-------------------------------------------------- 100%
concat :|-------------------------------------------------- 100%
spots read : 1,815,757,874
reads read : 3,631,515,748
reads written : 3,631,515,748
I am receiving errors listed below when I run fasterq-dump on sra files that were downloaded earlier using prefetch. Fasterq-dump is run with default settings, the only command line arguments being used are -p, -O and -t. The input data consists of relatively large files, but there is enough RAM and disk space. The errors are reported at the beginning of the join phase, which then proceeds as if nothing has happened. However I am not sure about the impact of these errors on the output data. Errors occur for approximately half of sra files. Very occasionally an additional error will be thrown after join phase processing has already started (see second example, error at 0.27% progress).
This problem is similar to issue #331, but I am reporting it against a newer version of sra-tools. Unfortunately, issue #331 does not offer any insights on the nature of the error, nor any workarounds.
Help will be greatly appreciated.
SRR12599535
lookup :|-------------------------------------------------- 100%
merge : 14446522576
join :| 0.00%2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 2591896 of 3086968
2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1035800 of 3086968
2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1554488 of 3086968
2022-11-05T20:14:19 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 2073192 of 3086968
-------------------------------------------------- 100%
concat :|-------------------------------------------------- 100%
spots read : 1,945,116,998
reads read : 3,890,233,996
reads written : 3,890,233,996
SRR12599536
lookup :|-------------------------------------------------- 100%
merge : 15131824452
join :| 0.00%2022-11-05T22:56:02 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 2419416 of 2881016
2022-11-05T22:56:02 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1935208 of 2881016
2022-11-05T22:56:02 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 1451000 of 2881016
0.27%2022-11-05T22:56:15 fasterq-dump.3.0.0 err: index.c get_nearest_offset() -> too many rounds pos = 969080 of 2881016
-------------------------------------------------- 100%
concat :|-------------------------------------------------- 100%
spots read : 1,815,757,874
reads read : 3,631,515,748
reads written : 3,631,515,748