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micans / mcl

MCL, the Markov Cluster algorithm, also known as Markov Clustering, is a method and program for clustering weighted or simple networks, a.k.a. graphs.
https://micans.org/mcl
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Cannot open out stream Error #6

Closed eli1199 closed 2 years ago

eli1199 commented 2 years ago

Hello,

I'm getting a strange error message from mcl. code and output can be found below:

$ mcl mclInput --abc -I 1.5 -o mclOutput .........[mcl] new tab created [mcl] pid 15159 ite ------------------- chaos time hom(avg,lo,hi) m-ie m-ex i-ex fmv 1 ................... 25.41 0.12 0.99/0.25/5.16 1.46 1.42 1.42 3 2 ................... 43.22 0.17 0.90/0.19/3.67 1.35 1.08 1.53 5 3 ................... 46.47 0.18 0.84/0.08/3.49 1.29 0.95 1.46 5 4 ................... 39.57 0.16 0.80/0.10/2.66 1.22 0.93 1.35 5 5 ................... 44.13 0.14 0.77/0.10/2.91 1.14 0.91 1.23 4 6 ................... 27.14 0.12 0.75/0.13/1.73 1.08 0.88 1.08 3 7 ................... 16.20 0.10 0.73/0.09/1.57 1.07 0.86 0.93 3 8 ................... 13.40 0.08 0.71/0.25/1.28 1.03 0.88 0.82 2 9 ................... 11.88 0.07 0.71/0.21/1.09 1.01 0.86 0.71 1 10 ................... 8.79 0.04 0.73/0.32/1.18 1.00 0.83 0.58 0 11 ................... 5.15 0.04 0.76/0.35/1.06 1.00 0.85 0.49 0 12 ................... 5.97 0.03 0.81/0.35/1.00 1.00 0.82 0.40 0 13 ................... 4.66 0.02 0.86/0.43/1.00 1.00 0.78 0.31 0 14 ................... 2.88 0.02 0.90/0.41/1.08 1.00 0.78 0.24 0 15 ................... 2.43 0.02 0.93/0.43/1.00 1.00 0.78 0.19 0 16 ................... 2.29 0.02 0.95/0.51/1.00 1.00 0.80 0.15 0 17 ................... 2.04 0.02 0.97/0.56/1.00 1.00 0.85 0.13 0 18 ................... 1.68 0.02 0.98/0.63/1.00 1.00 0.88 0.11 0 19 ................... 0.90 0.01 0.98/0.53/1.00 1.00 0.90 0.10 0 20 ................... 0.99 0.01 0.99/0.48/1.00 1.00 0.93 0.10 0 21 ................... 0.88 0.01 0.99/0.60/1.00 1.00 0.95 0.09 0 22 ................... 0.43 0.01 1.00/0.73/1.00 1.00 0.97 0.09 0 23 ................... 0.38 0.01 1.00/0.75/1.00 1.00 0.98 0.09 0 24 ................... 0.35 0.01 1.00/0.76/1.00 1.00 0.99 0.09 0 25 ................... 0.38 0.01 1.00/0.76/1.00 1.00 0.98 0.08 0 26 ................... 0.34 0.01 1.00/0.76/1.00 1.00 1.00 0.08 0 27 ................... 0.25 0.01 1.00/0.77/1.00 1.00 0.99 0.08 0 28 ................... 0.25 0.01 1.00/0.76/1.00 1.00 1.00 0.08 0 29 ................... 0.21 0.01 1.00/0.79/1.00 1.00 1.00 0.08 0 30 ................... 0.12 0.01 1.00/0.88/1.00 1.00 1.00 0.08 0 31 ................... 0.04 0.01 1.00/0.96/1.00 1.00 1.00 0.08 0 32 ................... 0.01 0.01 1.00/0.99/1.00 1.00 1.00 0.08 0 33 ................... 0.00 0.01 1.00/1.00/1.00 1.00 1.00 0.08 0 34 ................... 0.00 0.01 1.00/1.00/1.00 1.00 1.00 0.08 0 [mcl] jury pruning marks: <99,99,99>, out of 100 [mcl] jury pruning synopsis: <99.0 or perfect> (cf -scheme, -do log) [mcl parlour] cannot open out stream [mcl parlour] trying to fall back to default ___ [mcxIOopen] w stream cannae be opened

Anyone know what causes this kind of error? I've used this command with those arguments many times in the past and never had issues. Thank you.

micans commented 2 years ago

Hi, this is not an error on the mcl side, it is just not allowed to write its output. Most likely you do not have write permission in the place where you run mcl. You can test this by issuing in the shell for example (in the same place):

echo test > test.txt
eli1199 commented 2 years ago

Thank you @micans , running that test allowed me to realize that it was a 'disk quota exceeded' issue, and that is why the output files were not being produced. Thank you.