Error with r-rcpp during rafah step

[Former user]

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!

[Stanley Ho]

Not sure why the error code didnt format correctly above. Here’s the entirety of the rafah.log file.

Running host prediction mode
Indexing sequences from iphop_results/Wdir/split_input/
Processing AJ421943.1.fasta
Processed 1 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 88 OGs across 1 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    8386030   447.9   14550460   777.1   11684437   624.1
Vcells 2145114740 16366.0 2774702278 21169.3 2191067527 16716.6
[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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[Simon Roux]

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 ?

[Stanley Ho]

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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[Simon Roux]

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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[Stanley Ho]

It worked! Thanks a lot for investigating. I wonder why the conda package didn’t work for this.

[Simon Roux]

Good question, conda is still mysterious to me sometimes, but glad that it worked :-)

[Simon Roux]

Manual install of the R package in the conda environment seemed to fix the issue