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I hadn't used the NCBI command-line tools for a while, and just got back into it. But no matter where or how I run blastn now, I get an almost complete lack of response: just the initial "BLASTN 2.10.1+" header, then complete silence, forever. No timeout, no error. The situation is the same whether I use 2.6.1, 2.8.1, or 2.10.1, from Linux or the Windows bash subsystem, from my laptop at home or from my institution's cluster. So it's not network or firewall or anything -- at least not on my end. My command is:

blastn -task blastn -remote -db nt -query OTUs.subset.1 -out OTUs.subset.1.blast

I would normally be using more options, like outfmt, but I'm trying to do the simplest test I can.

Example sequences from the input file are:

>plantITS_OTU_96
GAACCTGCGGAAGGATCATTA.........................................................................................................ACAAAAATAAGAAAATTCTCAACGATGGATATCTAGGTTCCCATAACGATG
>plantITS_OTU_97
GAACCTGCGGAAGGATCATTAACACGT........................................................................................................................................................................................................................................GATATCTCGGTTCTCGCAACGATG

...where of course there are correct bases instead of the dots. The sequences BLAST just fine on the web.

The only way I know of to get more information out of this situation is by running strace, which shows me things like this:

recvfrom(4, "\r\215\325\204B`\350\327\256'/\213X\276\214\365\271#\25\177\261\327\314\270\33\251\337\370}}\256L"..., 40, 0, NULL, NULL) = 40
sendto(4, "\27\3\3\1\266\0\0\0\0\0\0\0\1f\16\343\304G\242\31r\177\265Z\236\210\270\1\213d\377\336"..., 443, 0, NULL, 0) = 443
recvfrom(4, 0x7ffff4533fb8, 5, 0, NULL, NULL) = -1 EAGAIN (Resource temporarily unavailable)
poll([{fd=4, events=POLLIN}], 1, 30000) = 1 ([{fd=4, revents=POLLIN}])
recvfrom(4, "\27\3\3\0031", 5, 0, NULL, NULL) = 5
recvfrom(4, "\r\215\325\204B`\350\330\265\255}\234Y^\266\360\207\275\205\232N\275<ua\253\372\366\2538d("..., 817, 0, NULL, NULL) = 817
time(NULL)                              = 1592752704 (2020-06-21T10:18:24-0500)
setsockopt(4, SOL_TCP, TCP_LINGER2, [-1], 4) = -1 ENOPROTOOPT (Protocol not available)

The first few times, I assumed the service was down, or I was having a network problem, or something like that, but I've been trying for over a week now on different platforms and from different IPs without getting anything different. What am I doing wrong? Thanks! The copies of 2.10.1 are the pre-compiled Linux binaries, and I believe I compiled the 2.8.1 myself a while back.

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