show the OS error message if a system call fails.įor now, I'll just merge some/all of single-end+unpaired libraries, to decrease their number.close files that are not being worked with anymore (2048 is a hard limit on our system, and I just reached it on the 51st library :) ).I wonder if it would be reasonably easy and useful in this case to: I have then increased my limit of open files to 2048 from the standard soft limit 1024, and. bin_reads contains 1046 files, of which 1020 are. I have also run fastQValidator on that file, and it returned 0 errors. I have also ran fqtools validate on that file, it reported "header mismatch" but that does not seem relevant at all. I have just recompressed that one file with slightly different options ( -fast, -best, -rsyncable - all of which should not matter other than re-creating the file), and still got this same error. Yes, it is reproducible - I tried -continue maybe five times, it's always the same message/library. Summary: this was an open files limit problem. I'm not sure if this is relevant, but corrected reads come from a metaspades.py -m 500 run (which could not handle that many libraries), and this failing spades.py run is now limited to -m 250. The file is readable, gunzip -test reports no problems on it. ![]() 25_0. suffix - it's a 900 MB file with exactly 6602328 reads (extendedFrags, a result of merging some paired reads with flash). The library #25 is probably the one with. = Error = system call for: "" finished abnormally, err code: -6 Spades: /spades/src/common/io/reads/binary_streams.hpp:62: virtual void io::BinaryFileSingleStream::reset(): Assertion `stream_.good()' failed.
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