I have two files that are not created when the command is restarting (portcullis.junctions.tab , portcullis.junctions.bed )

[sashulkaSh]

Hello!
I run command:

portcullis  full -t ${t} \
--bam_filter \
--orientation FR \
--strandedness unstranded \
-o ./portcullis2 \
${g} \
${bam}/*

I have two files that are not created when the command is restarting ...
portcullis.junctions.tab
portcullis.junctions.bed

wc -l portcullis.junctions.tab :
831341 portcullis.junctions.tab

These files were created for the first time, as well as when restarting:
wc -l */*tab :
371669 2-junc/portcullis_all.junctions.tab
164121 3-filt/portcullis_filtered.pass.junctions.tab
116171 3-filt/portcullis_filtered.selftrain.initialset.neg.junctions.tab
55726 3-filt/portcullis_filtered.selftrain.initialset.pos.junctions.tab
707687 total

At first I decided that portcullis.junctions.tab is a concatenate of all files 2-junc/portcullis_all.junctions.tab, 3-filt/portcullis_filtered.pass.junctions.tab, 3-filt/portcullis_filtered.selftrain.initialset.neg.junctions.tab, 3-filt/portcullis_filtered.selftrain.initialset.pos.junctions.tab , but the sum of the lines of these files is not equal to the number of lines portcullis.junctions.tab .....
What is this file and why is it not created in new runs (in the new folder)?
What file with junctions should I use in further work?

(I launched the same team on other data, but I could not get this files portcullis.junctions.tab , portcullis.junctions.bed anymore)

Thanks...