Error with r-rcpp during rafah step
Hi there,
I'm having trouble with getting iphop to run during the rafah tool. It gives me the "FileNotFoundError: [...] rafah_out/Full_Host_Predictions.tsv" error but I don't believe this issue is to do with running out of memory or the perl libraries (I added the update bioperl scripts already). When I look at rafah.log it appears the issue is to do with r-rcpp:
<pre>Error in rangerCpp(treetype, x, y, forest$independent.variable.names, : function 'Rcpp_precious_remove' not provided by package 'Rcpp' Calls: predict ... predict.ranger -> predict -> predict.ranger.forest -> rangerCpp Execution halted No such file or directory at /home/ubuntu/sdb/miniconda3/envs/iphop/lib/python3.8/site-packages/iphop/utils/RaFAH_v0.3.pl line 313. Parsing output of host prediction iphop_results/Wdir/rafah_out/Full_Host_Predictions.tsv ```
I've tried downgrading rcpp from 1.08 to 1.07/1.06 as well as downgrading iphop from 1.2 to 1.1 but this hasn't changed anything. Do you have any idea how to fix this?
P.S. Merry christmas!
Comments (7)
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repo owner Yikes, sorry I’ve never seen this issue with RaFAH in a conda install. I wonder if there is maybe something weird happening because you are only processing a single sequence (it shouldn’t be, but ..). Did you try the test dataset, and do you see the same error there ?
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I just tried the test dataset and got the same error in the log
Running host prediction mode Indexing sequences from iphop_results/Wdir/split_input/ Processing AJ421943.1.fasta Processing CP017905.1.fasta Processing IMGVR_UViG_3300013274_000001.fasta Processing IMGVR_UViG_3300013456_000001.fasta Processing MT657335.1.fasta Processed 5 Genomic Sequences Running Prodigal Indexing sequences from iphop_results/Wdir/rafah_out/Full_CDS_Prediction.faa Running hmmsearch. Query: iphop_results/Wdir/rafah_out/Full_CDS_Prediction.faa DB: Test_db/db/rafah_data/HP_Ranger_Model_3_Filtered_0.9_Valids.hmm Obtained 43644 ids from Test_db/db/rafah_data/HP_Ranger_Model_3_Valid_Cols.txt Parsing iphop_results/Wdir/rafah_out/Full_CDSxClusters_Prediction Detected 653 OGs across 5 genomic sequences Performing host prediction [1] "Loading Model from Test_db/db/rafah_data/MMSeqs_Clusters_Ranger_Model_1+2+3_Clean.RData" [1] "Reading input file iphop_results/Wdir/rafah_out/Full_Genome_to_OG_Score_Min_Score_50-Max_evalue_1e-05_Prediction.tsv" used (Mb) gc trigger (Mb) max used (Mb) Ncells 8386022 447.9 14550437 777.1 11684437 624.1 Vcells 2145248296 16367.0 2774702278 21169.3 2191973437 16723.5 [1] "Passing data to Random Forest using 16 threads" Error in rangerCpp(treetype, x, y, forest$independent.variable.names, : function 'Rcpp_precious_remove' not provided by package 'Rcpp' Calls: predict ... predict.ranger -> predict -> predict.ranger.forest -> rangerCpp Execution halted No such file or directory at /home/ubuntu/sdb/miniconda3/envs/iphop/lib/python3.8/site-packages/iphop/utils/RaFAH_v0.3.pl line 313. Parsing output of host prediction iphop_results/Wdir/rafah_out/Full_Host_Predictions.tsv
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repo owner That is weird, I will have to investigate. According to https://stackoverflow.com/questions/68416435/rcpp-package-doesnt-include-rcpp-precious-remove , it may be a case where the Rcpp package needs to be reinstalled. That would look something like:
source activate iphop_env
R
install.packages('Rcpp')
or
update.packages('Rcpp')
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It worked! Thanks a lot for investigating. I wonder why the conda package didn’t work for this.
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repo owner Good question, conda is still mysterious to me sometimes, but glad that it worked :-)
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repo owner - changed status to resolved
Manual install of the R package in the conda environment seemed to fix the issue
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Not sure why the error code didnt format correctly above. Here’s the entirety of the rafah.log file.