User: FGV

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FGV90
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Posts by FGV

<prev • 32 results • page 1 of 4 • next >
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Comment: C: GNU parallel error: Command line too long
... Hmmm, I think it is a `parallel` issue (or rather `execve`), since I can run the commands directly on the terminal. From what I understood, parallel uses `execve` to run the commands, and that has a much smaller buffer (apparently 20x smaller) than the terminal limit (seen as `getconf ARG_MAX`). ...
written 4 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... But it is exactly the `cat` that breaks the limit because I am doing it on several thousand files. I guess I could do the `cat` directly on the terminal (no `parallel`), and then use `parallel` to run all the alignments since these are the time intensive steps... ...
written 4 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... Well, the command is basically a `cat` of several files and then piped into MAFFT. I guess I could split the cat into several `cats`, and pipe it at the end.. but that is a bit error-prone and I'd like to avid it if possible. ...
written 4 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... What about making it more optimistic? :) ...
written 5 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... It is the list of arguments that is too large. ...
written 5 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... OK, does that mean that there is no way to increase the execve limit? What about making GNU parallel more optimistic (and not assume all characters have to be quoted)? :) Would it be possible to have an option for this? thanks, ...
written 5 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... But even if GNU parallel assumes quotes, the maximum argument length is still quite low. According to `getconf`, I should be able to use 2'621'440 characters (see post above). Why is GNU parallel limit 20 times lower than that? It seems I have 5 commands with length greater than 100'000 characters ...
written 6 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... As I said on another post, I actually have a script with all the commands that I pipe to parallel, and it is actually the first line that has 223188 characters. Also noticed that there are other lines that won't work either: 1020419 391943 223188 150854 146331 Strangely, I ext ...
written 10 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... Sure, it matches with the error message: $ parallel --max-line-length-allowed 131049 ...
written 10 days ago by FGV90
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Comment: C: GNU parallel error: Command line too long
... That is actually what I am doing... I have a file with the commands to run (several thousand) and I pipe it to parallel. It seems one of these commands is way too big... ...
written 10 days ago by FGV90

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