phylogenize error: BURST failed with error code 11

Community Plugin Support
1

Hi everyone! I am having some issues with BURST when I am trying to run phylogenize. Here is the output message of the error:

render.report(output_file = "report_phylogenize_young_vs_old", out_dir=".",type = "16S", which_phenotype="prevalence", which_envir="young", abundance_file="phylogenize_old_young_intestine.txt", metadata_file="Metadata_phylogenize_young_old.txt", sample_column="sample", input_format="tabular", burst_dir="/beegfs/group_dv/home/DDavila/bin",dset_column="dataset",ncl=10)
ncl: 10
type: 16S
out_dir: /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine
in_dir: /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine
data_dir: /beegfs/group_dv/home/DDavila/.R/3.5.1/R_LIBS_USER/phylogenize/extdata
abundance_file: phylogenize_old_young_intestine.txt
metadata_file: Metadata_phylogenize_young_old.txt
biom_file: test.biom
input_format: tabular
separate_metadata: FALSE
env_column: env
dset_column: dataset
sample_column: sample
phenotype_file:
db_version: midas_v1.2
which_phenotype: prevalence
which_envir: young
prior_type: uninformative
prior_file:
minimum: 3
treemin: 5
pctmin: 0.025
assume_below_LOD: TRUE
skip_graphs: FALSE
burst_dir: /beegfs/group_dv/home/DDavila/bin
linearize: FALSE
pryr: FALSE
prev_color_low: black
prev_color_high: orange2
spec_color_low: slateblue
spec_color_mid: gray50
spec_color_high: tomato
gene_color_absent: black
gene_color_present: slateblue2
separate_process: TRUE
biom_dir: /usr/local/bin/
error_to_file: TRUE
burst_16sfile: 16s_renamed.frn
burst_infile: input_seqs.txt
burst_outfile: output_assignments.txt
burst_cutoff: 0.985
burst_bin: burst12
use_rmd_params: FALSE
devel: FALSE
devel_pkgdir: package/phylogenize
relative_out_dir: /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine
single_dset: FALSE
working_dir: /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine
meas_err: TRUE
min_fx: 0

processing file: phylogenize-report.Rmd
|....... | 5%
ordinary text without R code

|............... | 9%
label: setup (with options)
List of 5
warning: logi FALSE message: logi FALSE
results: chr "hide" echo : logi FALSE
$ cache : logi TRUE

located abundance file: /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine/phylogenize_old_young_intestine.txt
located metadata file: /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine/Metadata_phylogenize_young_old.txt
Calling BURST with arguments: -r /beegfs/group_dv/home/DDavila/.R/3.5.1/R_LIBS_USER/phylogenize/extdata/16s_renamed.frn -fr -q /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine/input_seqs.txt -i 0.985 -o /beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine/output_assignments.txt
Quitting from lines 40-110 (phylogenize-report.Rmd)
Error in pz.error(paste0("BURST failed with error code ", r)) :
BURST failed with error code 11
In addition: Warning messages:
1: In dir.create(pz.options("out_dir")) :
'/beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine' already exists
2: In dir.create(pz.options("out_dir")) :
'/beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine' already exists
3: In dir.create(cache.d) :
'/beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine/cache' already exists
4: In dir.create(pz.options("out_dir")) :
'/beegfs/group_dv/home/DDavila/DDavilaR/dada2/Killifish/young_old_intestine' already exists

Could someone hwlp me to solve this? @pbradz
Thanks a lot in advance!

1 Like
2

Hi Francisco,

I had a similar issue. Check this post:

Maybe it may be useful for you.

Thanks,
Fernando

1 Like
3

Hi Francisco,

I think that error code indicates a segfault, which would suggest you need a different BURST binary for your architecture. If you have an older computer, for instance, it may not be compatible with the latest version of BURST since it uses some fancy optimizations that are dependent on having a particular chipset. You may have more luck downloading an older version of BURST (if necessary, renaming it “burst12” so phylogenize knows where to find it).

Let me know if this helps!

Best,
Patrick

P.S. Sorry for the delayed response; I’m traveling right now but will have a bit more time early next week.

2 Likes
4

Hi Patrick,

Thanks a lot for your suggestion. I will try and let you know.

Thanks again for taking your time to answer.

Best,

Daniel