Generating a map file for asv input for PICRUST2

1

Hi,

I would be most grateful for your help please. I am trying to generate the required files for downstream analyses with PICRUST2. I am referencing your github code on https://github.com/SchlossLab/Sze_SCFACRC_mBio_2019/blob/master/code/asv.sh
I have ran the mothur > make.shared(count = inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table , label = ASV, outputdir=asv/)
Setting output directory to: asv/

Output File Names:
asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.shared
asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.list

I am stuck at the rename.seqs section. I don’t seem to have any files with the suffix pick.pick.pick.map
[sample from Marc Sze code: map=$WORKDIR/crc.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.pick.map]

The only files that I have is the *.trim.contigs.good.unique.good.filter.unique.precluster.{name of sample}.map

The files that have with the .trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick. is as follows:

./asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.shared
./asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.list
./inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table

I am using mothur v.1.44.1

Could you please advise on how I can generate the map file please?

Thank you

2

Sorry, we don’t have much use for picrust2 (the premise that you can meaningfully infer function from taxonomy is pretty flawed - we used it to show that the method was limited). Since I don’t recall what input files it is looking for, I won’t be much help. If you could tell us what you need the files to do, we can probably get you closer.

Pat

3

Dear Pat,

Thank you very much for taking the time to reply.

I’m trying to generate a biom file whereby the first column has the same IDs as the IDs on the fasta file produced from pre.cluster

less inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta

>M04144_6_000000000-BYBVF_1_1111_2161_14902

TAC–GT-AG-GGG—GCA-A-G-C-G-T–T–AT-C-CGG-AT–TT-A-C-T–GG-GT–GT-A–AA-GG-GA-GC-G-TA-G-A-C-G-G–C-AT-G-G-C–AA-G-C-C-A–G-A-T-G–TG–A-AA-AC–C-C-AG-G-G–CT-C-AA-C-C-C-T-G-G-G-A-C–T-G–C-A–T-T-T–GG-A-A—C-T-G-T–CA–G-G-C-T-G-G-A-G-T–G–C-AG------GA-G-A–G-G-T-A—AG-C----GG–A–ATT–C-C-T-A-GT–GT-A-G-CG-GT-G–A-A-A–TG-C-GT-AG–AT-A-AT-A-G-G-A–G-G-A-AC-A-CC—AG–T-G–GC-GAA-G–G-C—G-G–C-T-T-A–CTG-G–AC-T-G—T-A-A-C-T–GA–CG-T-T-G-A-GG–C-T-CG-A-AA-G-C–G-TG–GG-G–AG-C-A-AA-CA-GG

M04144_6_000000000-BYBVF_1_2105_12039_11326

TAC–GT-AG-GGG—GCG-A-G-C-G-T–T–GT-C-CGG-AA–TG-A-T-T–GG-GC–GT-A–AA-GG-GC-GC-G-TA—G—G-G–C-CT-G-C-T–AA-G-T-C-T–G-A-A-G–TG–A-AA-GT–C-C-TG-C-T–TT-C-AA-G-G-T-G-G-GAA-G-A----G–C-T–T-T-G–GA-T-A—C-T-G-G–TG–G-G-C-T-G-G-A-G-T–G–C-AG------GA-G-A–G-G-A-A—AG-C----GG–A–ATT–A-C-C-G-GT–GT-A-G-CG-GT-G–A-A-A–TG-C-GT-AG–AG-A-TC-G-G-T-A–G-G-A-AC-A-CC–AGT----G–GC-GAA-G–G-C—G-G–C-T-T-T–CTG-G–AC-T-G—A-A-A-C-T–GA–CG-C-T-G-A-GG–C-G-CG-A-AA-G-C–G-TG–GG-G–AG-C-A-AA-CA-GG

mothur > make.biom(shared=/data/MMP_gutmicrobiome_2020_v2/MMP_gutmicrobiome_2020_v2/asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.shared , outputdir = /data/MMP_gutmicrobiome_2020_v2/asv/)

Setting output directory to: /data/MMP_gutmicrobiome_2020_v2/asv/

ASV

Output File Names:

/data/MMP_gutmicrobiome_2020_v2/asv/inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.ASV.biom

(base) ubuntu@liying-biggvl : /data/MMP_gutmicrobiome_2020_v2/asv $ biom validate-table -i inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.ASV.biom

Invalid format ‘Biological Observation Matrix 0.9.1’, must be ‘1.0.0’

Timestamp does not appear to be ISO 8601

The input file is not a valid BIOM-formatted file.

(base) ubuntu@liying-biggvl : /data/MMP_gutmicrobiome_2020_v2/asv $ biom convert -i inputfileMMPHC.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.ASV.ASV.biom -o temp_OTU_table.txt --table-type=“OTU table” --to-tsv

(base) ubuntu@liying-biggvl : /data/MMP_gutmicrobiome_2020_v2/asv $ biom convert -i temp_OTU_table.txt -o inputMMPHC.asv.biom --table-type=“OTU table” --to-json

(base) ubuntu@liying-biggvl : /data/MMP_gutmicrobiome_2020_v2/asv $ biom validate-table -i inputMMPHC.asv.biom

The input file is a valid BIOM-formatted file.

(base) ubuntu@liying-biggvl : /data/MMP_gutmicrobiome_2020_v2/asv $ biom head -i inputMMPHC.asv.biom

Constructed from biom file

#OTU ID NETS016 NETS025pre NETS029HCUOB2018 NETS031 NETS033

Otu00001 0.0 0.0 0.0 0.0 0.0

Otu00002 0.0 0.0 0.0 0.0 0.0

Otu00003 0.0 0.0 0.0 0.0 0.0

Otu00004 0.0 0.0 0.0 0.0 0.0

Otu00005 0.0 0.0 0.0 0.0 0.0

4

any resolution for this?
Did you get this?

I’m struggling with the same.
Id name from fasta is different from biom generated in Mothur

thanks,