ruqianl / sgcocaller Goto Github PK

Hi, I'm very interested in using this tool. I also get an issue, using 0.3.9 (see below). I tried again using prior versions (0.3.6, 0.3.4 and 0.3.3) and get the same error. I then installed on both a linux cluster, and a WSL version of Ubuntu locally and get the same issue. File path does not appear to be the issue for me

./sgcocaller xo \

--phased
--cmPmb 0.0001
possorted_genome_bam.bam
Cross.filt.recal.vcf
barcodes.tsv
BULK_1_sgco
2022-11-02T12:41:15-05:00{"": barcodes.tsv, "": possorted_genome_bam.bam, "--binSize": 2000, "--dissimThresh": 0.0099, "--notSortMtx": false, "": nil, "phase": false, "--lookBeyondSnps": 25, "--thetaREF": 0.1, "--outvcf": false, "--baseq": 13, "--minMAPQ": 20, "--threads": 4, "--stepSize": 200, "--cmPmb": 0.0001, "--chrom": nil, "--minPositiveSwitchScores": 8, "--minSwitchScore": 50.0, "": Cross.filt.recal.vcf, "": nil, "--barcodeTag": CB, "--maxUseNcells": nil, "": nil, "--maxExpand": 1000, "sxo": false, "autophase": false, "--maxTotalDP": 25, "xo": true, "--batchSize": nil, "--phased": true, "--templateCell": -1, "--help": false, "": nil, "--maxDP": 5, "--minDP": 1, "--minTotalDP": 10, "--maxDissim": 0.0099, "swphase": false, "--posteriorProbMin": 0.99, "--minSNPdepth": 1, "--thetaALT": 0.9, "<out_prefix>": BULK_1_sgco, "": nil}
2022-11-02T12:41:15-05:00 running sgcocaller 0.3.9
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

I then tried installing from source though ran into an error here also:

nimble install https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git
Downloading https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git using git
Verifying dependencies for [email protected]
Info: Dependency on docopt@any version already satisfied
Verifying dependencies for [email protected]
Info: Dependency on regex@>= 0.11.1 already satisfied
Verifying dependencies for [email protected]
Info: Dependency on unicodedb@>= 0.7.2 already satisfied
Verifying dependencies for [email protected]
Info: Dependency on hts@>= 0.3.4 already satisfied
Verifying dependencies for [email protected]
Info: Dependency on https://github.com/ruqianl/distributions.git@any version already satisfied
Verifying dependencies for [email protected]
Installing [email protected]
Building sgcocaller/sgcocaller using c backend
Prompt: Build failed for 'https://gitlab.svi.edu.au/biocellgen-public/[email protected]', would you like to try installing 'https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git@#head' (latest unstable)? [y/N]
Answer:
Tip: 12 messages have been suppressed, use --verbose to show them.
Error: Aborting installation due to build failure
ianc@PC51:~$ nimble install https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git --verbose
Downloading https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git using git
Cloning latest tagged version: v0.3.9
Info /tmp/nimble_1192/gitlabsvieduau_biocellgenpublicsgcocallergit/sgcocaller_1192.nims(5, 22) Warning: imported and not used: 'strutils' [UnusedImport]
Verifying dependencies for [email protected]
Reading official package list
Checking for docopt@any version
Info: Dependency on docopt@any version already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for regex@>= 0.11.1
Info: Dependency on regex@>= 0.11.1 already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for unicodedb@>= 0.7.2
Info: Dependency on unicodedb@>= 0.7.2 already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for hts@>= 0.3.4
Info: Dependency on hts@>= 0.3.4 already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for https://github.com/ruqianl/distributions.git@any version
Info: Dependency on https://github.com/ruqianl/distributions.git@any version already satisfied
Verifying dependencies for [email protected]
Installing [email protected]
Building sgcocaller/sgcocaller using c backend
Prompt: Build failed for 'https://gitlab.svi.edu.au/biocellgen-public/[email protected]', would you like to try installing 'https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git@#head' (latest unstable)? [y/N]
Answer: y
Downloading https://gitlab.svi.edu.au/biocellgen-public/sgcocaller.git using git
Info /tmp/nimble_1192/gitlabsvieduau_biocellgenpublicsgcocallergit_#head/sgcocaller_1192.nims(5, 22) Warning: imported and not used: 'strutils' [UnusedImport]
Verifying dependencies for sgcocaller@#head
Reading official package list
Checking for docopt@any version
Info: Dependency on docopt@any version already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for regex@>= 0.11.1
Info: Dependency on regex@>= 0.11.1 already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for unicodedb@>= 0.7.2
Info: Dependency on unicodedb@>= 0.7.2 already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for hts@>= 0.3.4
Info: Dependency on hts@>= 0.3.4 already satisfied
Verifying dependencies for [email protected]
Reading official package list
Checking for https://github.com/ruqianl/distributions.git@any version
Info: Dependency on https://github.com/ruqianl/distributions.git@any version already satisfied
Verifying dependencies for [email protected]
Installing sgcocaller@#head
Building sgcocaller/sgcocaller using c backend
Error: Build failed for package: sgcocaller
... Details:
... Execution failed with exit code 1
... Command: "/usr/bin/nim" c --noNimblePath -d:NimblePkgVersion=0.3.5 -d:release --path:"/home/ianc/.nimble/pkgs/docopt-0.7.0" --path:"/home/ianc/.nimble/pkgs/regex-0.20.0" --path:"/home/ianc/.nimble/pkgs/unicodedb-0.10.0" --path:"/home/ianc/.nimble/pkgs/hts-0.3.23" --path:"/home/ianc/.nimble/pkgs/distributions-0.1.0" -o:"/tmp/nimble_1192/gitlabsvieduau_biocellgenpublicsgcocallergit_#head/sgcocaller" "/tmp/nimble_1192/gitlabsvieduau_biocellgenpublicsgcocallergit_#head/src/sgcocaller.nim"
... Output: Hint: used config file '/etc/nim/nim.cfg' [Conf]
... Hint: system [Processing]
... Hint: widestrs [Processing]
... Hint: io [Processing]
... Hint: sgcocaller [Processing]
... Hint: os [Processing]
... Hint: strutils [Processing]
... Hint: parseutils [Processing]
... Hint: math [Processing]
... Hint: bitops [Processing]
... Hint: macros [Processing]
... Hint: algorithm [Processing]
... Hint: unicode [Processing]
... Hint: pathnorm [Processing]
... Hint: osseps [Processing]
... Hint: posix [Processing]
... Hint: times [Processing]
... Hint: options [Processing]
... Hint: typetraits [Processing]
... Hint: docopt [Processing]
... Hint: regex [Processing]
... Hint: tables [Processing]
... Hint: hashes [Processing]
... Hint: sequtils [Processing]
... Hint: types [Processing]
... Hint: sets [Processing]
... Hint: properties [Processing]
... Hint: properties_data [Processing]
... Hint: common [Processing]
... Hint: compiler [Processing]
... Hint: parser [Processing]
... Hint: exptype [Processing]
... Hint: scanner [Processing]
... Hint: exptransformation [Processing]
... Hint: nfatype [Processing]
... Hint: litopt [Processing]
... Hint: nodematch [Processing]
... Hint: types [Processing]
... Hint: types_data [Processing]
... Hint: nfa [Processing]
... Hint: deques [Processing]
... Hint: nfafindall [Processing]
... Hint: nfamatch [Processing]
... Hint: util [Processing]
... Hint: hts [Processing]
... Hint: utils [Processing]
... Hint: hts_concat [Processing]
... /home/ianc/.nimble/pkgs/hts-0.3.23/hts/private/hts_concat.nim(127, 9) Error: undeclared identifier: 'csize_t'

Hello, I tried to use sgcocaller v0.3.7 to detect COs in gametes using scRNA sequences from pollens, and our reference genome was phased. Here is the command I ran:

dir_to_sgcocaller/bin/sgcocaller xo --threads 8 --cmPmb 1 --phased merged.bam informative_SNPs.recode.vcf cb.list myprefix

Then I got an error as follows:

{"<barcodeFile>": cb.list, "<BAM>": merged.bam, "--binSize": 2000, "<referenceVCF>": nil, "phase": false, "--lookBeyondSnps": 25, "--thetaREF": 0.1, "--outvcf": false, "--baseq": 13, "--minMAPQ": 20, "--threads": 8, "--stepSize": 200, "--cmPmb": 1, "--chrom": nil, "--minPositiveSwitchScores": 8, "--minSwitchScore": 50.0, "<VCF>": informative_SNPs.recode.vcf, "<gtMtxFile>": nil, "--barcodeTag": CB, "<phasedSnpAnnotFile>": nil, "sxo": false, "--maxExpand": 1000, "--maxTotalDP": 25, "xo": true, "--phased": true, "--templateCell": -1, "--help": false, "<SNPPhaseFile>": nil, "--maxDP": 5, "--minDP": 1, "--minTotalDP": 10, "--maxDissim": 0.0099, "swphase": false, "--posteriorProbMin": 0.99, "--minSNPdepth": 1, "--thetaALT": 0.9, "<out_prefix>": rbrevi_test, "<phaseOutputPrefix>": nil}
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

The error message looks like from Nim, which I am not quite familiar with. Can you give me a clue about how to solve this?

"Tuning" parameters not "tunning"