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.

Dear ClipCrop developers,

I appreciate your great effort to a very interesting (and hopefully very useful) program, ClipCrop.
I would like to use ClipCrop, however, a problem was occurred when I tried to install ClipCrop as described in the README page.

$ npm install clipcrop
npm WARN install Refusing to install clipcrop as a dependency of itself

Could you tell me how can I resolve the problem?

Sincerely yours,

Tsuyoshi Hachiya @ Keio University

[23] clipcrop

INPUT INFORMATION

SAM FILE : 8.sam

FASTA FILE : /usr/local/bin/ref/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa

JSON FILE : null

OUTPUT DIR : /analysis/120704/8/23_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 : 8

node /usr/local/bin/node_modules/clipcrop/subs/rawbreaks.js 8.sam --parallel 8
sort -k10,10
node /usr/local/bin/node_modules/clipcrop/subs/cluster_breaks.js fastq 2 10 5 10
node /usr/local/bin/node_modules/clipcrop/subs/cluster_breaks.js bed 2 10 5 10
node /usr/local/bin/node_modules/clipcrop/subs/bpfastagen.js /analysis/120704/8/23_clipcrop/bp.bed /usr/local/bin/ref/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa -l 1000 -j
path.existsSync is now called fs.existsSync.
bwa index /analysis/120704/8/23_clipcrop/bp.fa
bwa aln -t 8 /analysis/120704/8/23_clipcrop/bp.fa /analysis/120704/8/23_clipcrop/bp.fastq >/analysis/120704/8/23_clipcrop/mapped.sai
bwa samse -f /analysis/120704/8/23_clipcrop/mapped.sam /analysis/120704/8/23_clipcrop/bp.fa /analysis/120704/8/23_clipcrop/mapped.sai /analysis/120704/8/23_clipcrop/bp.fastq
node /usr/local/bin/node_modules/clipcrop/subs/sam2sv.js /analysis/120704/8/23_clipcrop/mapped.sam
sort -k1,1
node /usr/local/bin/node_modules/clipcrop/subs/cluster_svinfo.js /usr/local/bin/ref/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa /analysis/120704/8/23_clipcrop 10 10
FAILED.

Why become FAILED?
I would appreciate it if you would teach me.

How fast does this program run?

I ran it on a ~150 GB BAM file and it finished in about 30 seconds or so which I think is far too quick and did not provide any entries in bp.fa. The mapped.sam and the all.bed just contain header information, despite reporting success. Any idea what is going on?

Lowering the min BP cluster size didn't add any more results, still nothing.

-John

INPUT INFORMATION

SAM FILE : X306_Merged_Lanes_realigned.bam

FASTA FILE : ./hg19.fa

JSON FILE : null

OUTPUT DIR : X306

BP FILTER PROCESSES : 2

MAX BREAKPOINT DIFF : 2

MIN BP CLUSTER SIZE : 5

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 : 2

node /lustre/scratch/ozborn/schroeder/ngs/clipcrop/shinout-clipcrop-421d175/subs/rawbreaks.js X306_Merged_Lanes_realigned.bam --parallel 2
node /lustre/scratch/ozborn/schroeder/ngs/clipcrop/shinout-clipcrop-421d175/subs/bpfastagen.js X306/bp.bed ./hg19.fa -l 1000 -j
bwa index X306/bp.fa
bwa aln -t 2 X306/bp.fa X306/bp.fastq >X306/mapped.sai
bwa samse -f X306/mapped.sam X306/bp.fa X306/mapped.sai X306/bp.fastq
node /lustre/scratch/ozborn/schroeder/ngs/clipcrop/shinout-clipcrop-421d175/subs/cluster_svinfo.js ./hg19.fa X306 10 10
SUCCEEDED