DepracationWarning 'root' errors plus others cause Clipcrop to exit

[bibbers93]

Good morning, I have recently installed nvm and clipcrop, and I believe this is as per your manual's instructions on to my local server, however I am having errors printed to screen, and as I have never used nvm/ node.js before I would like your help on trying to figure out the problem... (Apologies in advance for the long list of errors copy and pasted from my terminal, found below)

I am able to submit the following command to the command line

$ /<PATH>/clipcrop.js BLUE1.all.sam /<PATH>/hg38.fa --dir ../CLIPCROP/ --mapper bwa --mapper_threads 32

to which I get the following INPUT INFORMATION printed to screen followed by a series of warnings

#############################
# INPUT INFORMATION
# SAM FILE            : MY.SAM
# FASTA FILE          : /disk/home/HG38/hg38.fa
# JSON FILE           : null
# OUTPUT DIR          : ../CLIPCROP/
# BP FILTER PROCESSES : 8
# MAX BREAKPOINT DIFF : 2
# MIN BP CLUSTER SIZE : 10
# MIN MEAN BASE QUAL  : 5
# MIN SEQ LENGTH      : 10
# BASES AROUND BREAK  : 1000
# MAX SV DIFF         : 10
# MIN SV CLUSTER SIZE : 10
# MAPPER              : bwa
# MAPPER THREADS      : 32
#############################
(node:45425) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45431) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45432) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45439) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45445) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45452) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45459) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'
(node:45466) [DEP0016] DeprecationWarning: 'root' is deprecated, use 'global'

and when I open a new terminal and use the $top command I can see that there are several procedures running on my system under the name "node" which after a few hours changes to "sort" and sort -k10,10 is printed to my screen only to be followed with

/disk/home/s1667153/node_modules/clipcrop/subs/cluster_breaks.js:124
    result.cluster[LR].push(current);
                       ^

TypeError: Cannot read property 'push' of undefined
    at LineStream.<anonymous> (/disk/home/s1667153/node_modules/clipcrop/subs/cluster_breaks.js:124:24)
    at LineStream.emit (events.js:182:13)
    at LineStream.emit (/disk/home/s1667153/node_modules/linestream/LineStream.js:224:15)
    at LineStream.emitLineWithoutFilter [as emitLine] (/disk/home/s1667153/node_modules/linestream/LineStream.js:248:8)
    at /disk/home/s1667153/node_modules/linestream/LineStream.js:100:12
    at Array.forEach (<anonymous>)
    at Socket.<anonymous> (/disk/home/s1667153/node_modules/linestream/LineStream.js:99:11)
    at Socket.emit (events.js:182:13)
    at addChunk (_stream_readable.js:283:12)
    at readableAddChunk (_stream_readable.js:260:13)
/disk/home/s1667153/node_modules/clipcrop/subs/cluster_breaks.js:124
    result.cluster[LR].push(current);
                       ^

TypeError: Cannot read property 'push' of undefined
    at LineStream.<anonymous> (/disk/home/s1667153/node_modules/clipcrop/subs/cluster_breaks.js:124:24)
    at LineStream.emit (events.js:182:13)
    at LineStream.emit (/disk/home/s1667153/node_modules/linestream/LineStream.js:224:15)
    at LineStream.emitLineWithoutFilter [as emitLine] (/disk/home/s1667153/node_modules/linestream/LineStream.js:248:8)
    at /disk/home/s1667153/node_modules/linestream/LineStream.js:100:12
    at Array.forEach (<anonymous>)
    at Socket.<anonymous> (/disk/home/s1667153/node_modules/linestream/LineStream.js:99:11)
    at Socket.emit (events.js:182:13)
    at addChunk (_stream_readable.js:283:12)
    at readableAddChunk (_stream_readable.js:260:13)
events.js:167
      throw er; // Unhandled 'error' event
      ^

Error: write EPIPE
    at WriteWrap.afterWrite [as oncomplete] (net.js:788:14)
Emitted 'error' event at:
    at Socket.onerror (_stream_readable.js:690:12)
    at Socket.emit (events.js:182:13)
    at onwriteError (_stream_writable.js:431:12)
    at onwrite (_stream_writable.js:456:5)
    at _destroy (internal/streams/destroy.js:40:7)
    at Socket._destroy (net.js:613:3)
    at Socket.destroy (internal/streams/destroy.js:32:8)
    at WriteWrap.afterWrite [as oncomplete] (net.js:790:10)

and the programme then exists. Have I done something wrong with installing nvm or clipcrop? Also, at this moment in time I do not have a JSON file of my ref.fasta as I cannto get fastareader to work (which is why I'm thinking I haven't installed nvm properly.