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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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random tree error report #567

Closed sadiexiaoyu closed 1 year ago

sadiexiaoyu commented 1 year ago

Dear inferCNV,

thanks for the cool software! I am trying to run inferCNV using tumor_subcluster_partition_method='random_trees', but I got the error report like in the following:

Could you please give me any suggestion?

Thanks in advance!

Best, sadiexiaoyu

unique grps: 1,,2,

grp: 1 contains idx: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130

subset_clade_name: normal.1.1.1.1

WARN [2023-06-25 08:58:44] -not exceeding max recursion depth.

grp: 2 contains idx: 20,74

subset_clade_name: normal.1.1.1.2

WARN [2023-06-25 08:58:44] normal.1.1.1.2 size of 2 is too small to recurse on

grp: 2 contains idx: 25,71,79,81,93,112,127,136

subset_clade_name: normal.1.1.2

WARN [2023-06-25 08:58:44] normal.1.1.2 size of 8 is too small to recurse on

grp: 2 contains idx: 11,25,38,46,47,59,70,86,88,105,111,138

subset_clade_name: normal.1.2

unique tumor clade name: normal.1.2

INFO [2023-06-25 08:58:45] random trees, using 12 parallel threads

Error in socketAccept(socket = socket, blocking = TRUE, open = "a+b", :

all connections are in use

sadiexiaoyu commented 1 year ago

Hi,

I just fix it. The error was due to the setting of using 12 parallel threads. It is too large. When change the num_threads to a smaller number, e.g., 4, then it is ok.