Hello,

I'm trying to build a very large tree from a manually constructed distance matrix (11478 x 11478) using the PHYLIPNEW fneighbor program on a server. This is my first time using EMBOSS softwares and also Phylip

VCprot_refseqprot_pw.dm = distance matrix. Original command:

fneighbor -datafile VCprot_refseqprot_pw.dm  -outfile VCprot_refseqprot_pw.txt -treetype n -treeprint N

Error output:

Phylogenies from distance matrix by N-J or UPGMA method
Error: Distance file VCprot_refseqprot_pw.dm: line 11445 Row '1698712' has 90329996 values in square format
Error: Distances file found 3608 rows, expected 11478
Error: Unable to read distances file 'VCprot_refseqprot_pw.dm'
Died: fneighbor terminated: Bad value for '-datafile' and no prompt

Attempted debugging so far: I subsampled my dataset 5 times into square matrices with the following number of rows (7, 94, 841, 2913, 8187) - each time the program works perfectly and I get a neighbor-joining tree as expected.

Additionally, '1698712' is in the subsampled dataset as well so I'm not sure the error is anything to do with this row in particular.

Any thoughts on where this error might be coming from or more debugging suggestions are most welcome! Thank you very much in advance.