Step 3: Combining and annotating the blast files with orthogroup info error

[rac266]

Hello,

Thanks for creating Genespace! My current Genespace run is failing at step 3. I ran into the issue before with my previous version of genespace (v1.1.4), and after reading similar issues (#70 and #81) I downloaded the most recent version (v1.1.9) but am still running into the same error. Also, all created folders have output except for the riparian and dotplot folders.

library(GENESPACE) gpar <- init_genespace(

• wd = "/path/to/workingDir",
• path2mcscanx = "/path/to/MCScanX/") Checking Working Directory ... PASS: /path/to/workingDir Checking user-defined parameters ... Genome IDs & ploidy ... species1_AstMex3_surface_GCA_023375975.1: 1 species2_AstMex3_Molino_GCA_023375845.1 : 1 species3_AstMex3_Tinaja_GCA_023375835.1 : 1 species4_AMEX_1.1_GCA_019721115.1 : 1 Outgroup ... NONE n. parallel processes ... 14 collinear block size ... 5 collinear block search radius ... 25 n gaps in collinear block ... 5 synteny buffer size... 100 only orthogroups hits as anchors ... TRUE n secondary hits ... 0 Checking annotation files (.bed and peptide .fa): species1_AstMex3_surface_GCA_023375975.1: 27065 / 27065 geneIDs exactly match (PASS) species2_AstMex3_Molino_GCA_023375845.1 : 26293 / 26293 geneIDs exactly match (PASS) species3_AstMex3_Tinaja_GCA_023375835.1 : 27295 / 27295 geneIDs exactly match (PASS) species4_AMEX_1.1_GCA_019721115.1 : 27244 / 27244 geneIDs exactly match (PASS) Checking dependencies ... Found valid path to OrthoFinder v2.54: orthofinder Found valid path to DIAMOND2 v2.16: diamond Found valid MCScanX_h executable: /path/to//MCScanX//MCScanX_h gpar <- run_genespace(gsParam = gpar)

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1. Running orthofinder (or parsing existing results) Checking for existing orthofinder results ... ... found existing run, not re-running orthofinder

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2. Annotated/concatenated bed file exists

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3. Combining and annotating the blast files with orthogroup info ...

   Chunk 1 / 1 (01:43:15 PM) ...

   Error in rbindlist(mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : Item 1 of input is not a data.frame, data.table or list In addition: Warning message: In mclapply(1:nrow(chnk), mc.cores = nCores, function(i) { : all scheduled cores encountered errors in user code

Also, example headers for both the peptide and bed files are below:

head species1_AstMex3_surface_GCA_023375975.1.bed 1 45362 56004 ENSAMXG00025000236 1 64624 101667 ENSAMXG00025000257 1 103026 114134 ENSAMXG00025000258 1 123301 137874 ENSAMXG00025000259

head species1_AstMex3_surface_GCA_023375975.1.fa

ENSAMXG00025000109 CVRHDSHQVFGAFSSDPFRVSNSCYGTGETFLFTFDPEFKTFCWSGENSYFVRGFLDSLQ MGGGGGGPFGLWLDADLCRGSTFSCNTFRNQPLSPLQDFTIRAVEVWTFL ENSAMXG00025000110

[jtlovell]

ok! new error. can you re-run with just one core init_genespace(nCores = 1,...) and post the output? This will produce a more informative error. To help troubleshoot, if you are ok with it, would you mind sharing your input /bed and /peptide directories? If so, email (jlovell[at]hudsonalpha.org) or dm me on twitter and I'll send the link

[rac266]

Sounds good, thanks! I will send the files to your email. Below is the error with just 1 core:

3. Combining and annotating the blast files with orthogroup info ... Error in fwrite(x, file = filepath, showProgress = F, quote = F, sep = "\t") : Compression in fwrite uses zlib library. Its header files were not found at the time data.table was compiled. To enable fwrite compression, please reinstall data.table and study the output for further guidance.

[jtlovell]

hmmm. that sounds like a pretty straightforward issue ... can you try to re-install data.table?

[rac266]

Ah I see. Good news is updating data.table worked. Thank you! The plots look great.