Weird rectangle output

[weishwu]

If I run rectangle directly on my epiread it says: "[main_rectangle:79] Error, rectangle cannot cross chromosomes". The manual does not say the input has to be chromosome split.
If I run it on a subset of the epiread in chr1, it finishes but the output looks weird. The output simply appends a 9th column to the epiread file and the 9th column is a string of 1,020,893 Ns.

My epiread input:

1	K00135:125:HFV57BBXX:1:1223:20618:2404	2	-	39154135	C	.	.
1	K00135:125:HFV57BBXX:1:1223:20618:2404	1	-	39154135	C	.	.
1	K00135:125:HFV57BBXX:3:2211:8044:44482	1	+	47760131	C	.	.
1	K00135:125:HFV57BBXX:1:2212:23673:26898	1	-	61731684	CCC	.	.
1	K00135:125:HFV57BBXX:1:2212:23673:26898	2	-	61731684	CCC	.	.
1	K00135:125:HFV57BBXX:1:2109:1702:26318	1	-	69191536	TTTCCCC	.	.
1	K00135:125:HFV57BBXX:3:1109:11759:18599	2	-	173991209	C	.	.
1	K00135:125:HFV57BBXX:3:1109:11759:18599	1	-	173991209	C	.	.

My rectangle command-line:

biscuit_0_3_16_linux_amd64 rectangle -o epiread_rslM1Li_chr1_epiread_matrix Mus_musculus.GRCm38.dna_sm.primary_assembly.fa epiread_rslM1Li_chr1.epiread