Execution halted

[kuzman1306]

Dear Sanrrone,

I attempted to use GGisy, but I am getting the error (see below). From some reason, only one blast hit was generated (see output table attached).

I wonder if you could help me here.

Thank you in advance.

Sincerely

Nemanja

ubuntu@dynamiceinstein-674ae:/mnt/volume/GGisy$ sudo python3.8 GGisy.py -r example/genome1.fna -q example/genome2.fna


Building a new DB, current time: 09/28/2022 11:56:49
New DB name:   /mnt/volume/GGisy/ref
New DB title:  example/genome1.fna
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 10000000
[synteny.txt](https://github.com/Sanrrone/GGisy/files/9664650/synteny.txt)
00B
Adding sequences from FASTA; added 18 sequences in 0.0142639 seconds.
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘varhandle’

The following object is masked from ‘package:S4Vectors’:

    unfactor

Error in if (dat.col[i, 1] == chr1.s) { :
  missing value where TRUE/FALSE needed
Calls: circos
Execution halted

synteny.txt

[Sanrrone]

Hi @kuzman1306,
I updated the code, you were right, its a bug related when the sequences are too similar (and no reverse synteny is found).
try again updating GGisy.py.

regards,
Sandro

[kuzman1306]

Hi Sandro,

Thank you for your update. Unfortunately, only one blast hit was produced again. Please see below the outcome.

Regards,

Nemanja

sudo python3.8 GGisy.py -r example/genome1.fna -q example/genome2.fna


Building a new DB, current time: 09/29/2022 15:08:23
New DB name:   /mnt/volume/GGisy/ref
New DB title:  example/genome1.fna
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 18 sequences in 0.0149012 seconds.
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘varhandle’

The following object is masked from ‘package:S4Vectors’:

    unfactor

null device
          1

[Sanrrone]

Hi,
it is, is because the sequences are the same (I believe I just change one nucleotide).
is not an error.

regards

[kuzman1306]

Hi Sandro,

I attached the output file. It seems only one contig from each example genome were compared.

I also tried the script with my data, but I am getting the following error:

Error in read.table(handlefile, sep = "\t", stringsAsFactors = F, check.names = F) :
no lines available in input
Execution halted

I checked blast, it is installed on my machine ant it functions fine. Do you maybe know what could be the problem?
synteny.txt

Best regards,

Nemanja

[VNF1981]

Hi there,
Can't figure out what is the following error. First I thought it should be related to memory but I am getting the same error when I use 320 Gb of RAM. Any help would be highly appreciated

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘varhandle’

The following object is masked from ‘package:S4Vectors’:

unfactor

Error in read.table(handlefile, sep = "\t", stringsAsFactors = F, check.names = F) :
no lines available in input
Execution halted
slurmstepd: error: Detected 1 oom-kill event(s) in StepId=57785585.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.

[Sanrrone]

Hi,
could you give the input files to reproduce the bug?

Best,
Sandro

[VNF1981]

Hey Sandro,

Sure! I would appreciate it. But as this data has not been published yet, can I email a GDrive link to [email protected]?

[Sanrrone]

@VNF1981 it is not neccesary whole data, maybe just one short contig? try it and let me know if the error persist.

regards

[Sanrrone]

Hi!, I updated the code, could you try again?