batch run DBGWAS failed
Hello,
Thank you for developing this tool. It brings me hope of my data analysis. I work on bacterial genomics, and have run DBGWAS on 12 different phenotypic trait. Here is the command I use for 12 traits:
#! /bin/bash
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/cb -output /agro30/outputs/cb
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/chl -output /agro30/outputs/chl
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/cip -output /agro30/outputs/cip
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/ery -output /agro30/outputs/ery
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/growthAB -output /agro30/outputs/growthAB
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/growthTSB -output /agro30/outputs/growthTSB
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/K84 -output /agro30/outputs/K84
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/mot -output /agro30/outputs/mot
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/rif -output /agro30/outputs/rif
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/s10 -output /agro30/outputs/s10
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/tet -output /agro30/outputs/tet
docker run --rm -it -v /Users/cDBGWAS/agro30:/agro30 leandroishilima/dbgwas:0.5.4 -strains /aro30/strains30/va30 -output /agro30/outputs/va30
However, 5 of them succeeded and 7 of them failed. Here are error messages: ~/cDBGWAS/agro30/outputs/gwas_loop.txt:13699: [FATAL ERROR] Error executing /dbgwas/bin/DBGWAS_lib//phantomjs /dbgwas/bin/DBGWAS_lib//render_graph.js /agro30/outputs/mot/visualisations/components/comp_0.html /agro30/outputs/mot/visualisations/components/comp_0.html.png. Exit status: 9 ~/cDBGWAS/agro30/outputs/gwas_loop.txt:13699: [FATAL ERROR] Error executing /dbgwas/bin/DBGWAS_lib//phantomjs /dbgwas/bin/DBGWAS_lib//render_graph.js /agro30/outputs/mot/visualisations/components/comp_0.html /agro30/outputs/mot/visualisations/components/comp_0.html.png. Exit status: 9 ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33449: [FATAL ERROR] Error executing /dbgwas/bin/DBGWAS_lib//phantomjs /dbgwas/bin/DBGWAS_lib//render_graph.js /agro30/outputs/tet/visualisations/components/comp_0.html /agro30/outputs/tet/visualisations/components/comp_0.html.png. Exit status: 9 ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33449: [FATAL ERROR] Error executing /dbgwas/bin/DBGWAS_lib//phantomjs /dbgwas/bin/DBGWAS_lib//render_graph.js /agro30/outputs/tet/visualisations/components/comp_0.html /agro30/outputs/tet/visualisations/components/comp_0.html.png. Exit status: 9 ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33510: gsl: brent.c:202: ERROR: function value is not finite 0.00% ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33511: Default GSL error handler invoked. ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33513: Error in file(file, "r") : cannot open the connection ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33521: [FATAL ERROR] Error executing Rscript --vanilla /dbgwas/bin/DBGWAS_lib//DBGWAS.R /dbgwas/bin/DBGWAS_lib/ /agro30/outputs/va30/step1 /agro30/outputs/va30/step1/bugwas_input.id_phenotype bugwas_out /dbgwas/bin/DBGWAS_lib//gemma.0.93b 0.01 2>&1. Exit status: 256 ~/cDBGWAS/agro30/outputs/gwas_loop.txt:33521: [FATAL ERROR] Error executing Rscript --vanilla /dbgwas/bin/DBGWAS_lib//DBGWAS.R /dbgwas/bin/DBGWAS_lib/ /agro30/outputs/va30/step1 /agro30/outputs/va30/step1/bugwas_input.id_phenotype bugwas_out /dbgwas/bin/DBGWAS_lib//gemma.0.93b 0.01 2>&1. Exit status: 256
Can anyone please help me on how to interpret the error messages? What might go wrong? I do have two traits, with each of them only have one value being non-zero, all others are 0. Not sure if this will be an issue. The rest 5 failed traits all have normal values.
All genetic data are the same for each command. The only difference is the phenotypic traits.
Another question is on understanding the output. For the successful one, there is a file called all_comps_nodes_info.tsv In this file, the first column is Compid, see following screen short. In this case, the table has 1260 Compid, How does DBGWAS define Compid. The input I feed to DBGWAS command is 30 complete genome assembly. Each genome assembly contains one linear chromosome and one circular chromosome, and at least 2 plasmids. All assembly quality are very good. I want to generate a manhattan plot, so I want to merge compid to its corresponding either chromosome or plasmid. Is there a way for me to tell which Compid is from which genetic elements?
Really appreciate your help and suggestions.
Best, Limin