Problem with loadSQM in local machine

[lokyimandy]

Hi, I ran the project at University's cluster, and I ran sqm2tables.py squeezemeta_sc_dna squeezemeta_sc_dna/results/tables before transferring the results directory, SqueezeMeta_conf.pl and intermediate/contigsinbins under the project name of squeezemeta_sc_dna to local machine

I followed previous posts about installing SQMtools in local machine by compressing the file SqueezeMeta/lib/SQMtools using tar- zcvf SQMtools.tar.gz SQMtools

I have intalled the packages as following:

install.packages("doMC")
install.packages("ggplot2")
install.packages("data.table")
install.packages("reshape2")
install.packages("BiocManager")
BiocManager::install("pathview")
BiocManager::install('org.Hs.eg.db')

When I ran install.packages("~/Desktop/Disinfection(Bimonthly_P2)/Result/SQMtools.tar.gz", repos = NULL, type = "source"), I got the following error:

_Error in rawToChar(info) : embedded nul in string: '30 mtime=1675449930.372204666\n74 LIBARCHIVE.xattr.com.apple.quarantine=MDA4MjswMDAwMDAwMDtmaWxlemlsbGE7\n62 SCHILY.xattr.com.apple.quarantine=0082;00000000;filezilla;\n133 LIBARCHIVE.xattr.com.apple.macl=BQBo6XxUSUBEvac46k0E5r1TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n105 SCHILY.xattr.com.apple.macl=\005\0h\xe9|TI@D\xbd\xa78\xeaM\004\xe6\xbdS\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\n' Warning in install.packages : installation of package ‘/Users/lokyitang/Desktop/Disinfection(BimonthlyP2)/Result/SQMtools.tar.gz’ had non-zero exit status

Anyway, I tried devtools::install_local("SQMtools.tar.gz"), and it seems successful except skipping the pathview package:

Skipping 1 packages not available: pathview ── R CMD build ────────────── ✔ checking for file ‘/private/var/folders/mj/ggsv7h6d4gn6bh7z50nctz480000gn/T/RtmpAhFqZy/remotes13eb774ad8b6/SQMtools/DESCRIPTION’ ... ─ preparing ‘SQMtools’: ✔ checking DESCRIPTION meta-information ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories NB: this package now depends on R (>= 3.5.0) WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘SQMtools/data/Hadza.RData’ ─ building ‘SQMtools_1.6.0.tar.gz’

• installing source package ‘SQMtools’ ... using staged installation R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading * help installing help indices building package indices testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
• DONE (SQMtools)

So I started loading the project using SQMtools, unfortunately no matter I run scd = loadSQM('squeezemeta_sc_dna', engine = 'data.table') or scd = loadSQM('squeezemeta_sc_dna') , it gave me this error:

_Generating tabular outputs for project in squeezemeta_sc_dna sh: /home/lytangaa/miniconda3/envs/env_mamba/envs/SqueezeMeta/SqueezeMeta/utils/sqm2tables.py: No such file or directory Error in loadSQM("squeezemeta_scdna", engine = "data.table") : An error occurred while running sqm2tables.py In addition: Warning message: In system(command) : error in running command

The path of sqm2table.py is in the cluster. Previous posts mentioned that there is no need to install Squeezemeta in local machine, so I really don't know how to fix it. Sorry for being so lengthy, just want to provide more information as I am not sure where the problem is. Thank you for offering help.

[fpusan]

Hi! You need to run sqm2tables.py in your cluster, before copying the project to your local computer

[lokyimandy]

Thank you for your prompt reply. Yes, I did. I ran it in the cluster before transferring the files to the local computer.

[fpusan]

What is the content of the squeezemeta_sc_dna/results/tables directory?

[lokyimandy]

metag_stw.COG.abund.tsv metag_stw.COG.bases.tsv metag_stw.COG.copyNumber.tsv metag_stw.COG.cov.tsv metag_stw.COG.names.tsv metag_stw.COG.tpm.tsv metag_stw.KO.abund.tsv metag_stw.KO.bases.tsv metag_stw.KO.copyNumber.tsv metag_stw.KO.cov.tsv metag_stw.KO.names.tsv metag_stw.KO.tpm.tsv metag_stw.PFAM.abund.tsv metag_stw.PFAM.bases.tsv metag_stw.PFAM.copyNumber.tsv metag_stw.PFAM.cov.tsv metag_stw.PFAM.tpm.tsv metag_stw.RecA.tsv metag_stw.bin.tax.tsv metag_stw.class.allfilter.abund.tsv metag_stw.class.nofilter.abund.tsv metag_stw.class.prokfilter.abund.tsv metag_stw.contig.sequences.tsv metag_stw.contig.tax.allfilter.tsv metag_stw.contig.tax.nofilter.tsv metag_stw.contig.tax.prokfilter.tsv metag_stw.family.allfilter.abund.tsv metag_stw.family.nofilter.abund.tsv metag_stw.family.prokfilter.abund.tsv metag_stw.genus.allfilter.abund.tsv metag_stw.genus.nofilter.abund.tsv metag_stw.genus.prokfilter.abund.tsv metag_stw.order.allfilter.abund.tsv metag_stw.order.nofilter.abund.tsv metag_stw.order.prokfilter.abund.tsv metag_stw.orf.sequences.tsv metag_stw.orf.tax.allfilter.tsv metag_stw.orf.tax.nofilter.tsv metag_stw.orf.tax.prokfilter.tsv metag_stw.phylum.allfilter.abund.tsv metag_stw.phylum.nofilter.abund.tsv metag_stw.phylum.prokfilter.abund.tsv metag_stw.species.allfilter.abund.tsv metag_stw.species.nofilter.abund.tsv metag_stw.species.prokfilter.abund.tsv metag_stw.superkingdom.allfilter.abund.tsv metag_stw.superkingdom.nofilter.abund.tsv metag_stw.superkingdom.prokfilter.abund.tsv

[lokyimandy]

On no, I think I know what the problem is. I changed the project name from metag_stw to squeezemeta_sc_dna in the cluster before, that why it didn't recognise the files. I changed the name to metag_stw again and it works! Thank you for your reply.

[fpusan]

Glad to hear! Closing issue