Error with remove.otus

mothur bugs
1

I got the following output when I used remove.otus:

Linux version

Using ReadLine,Boost,HDF5,GSL

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Batch Mode



mothur > remove.otus(accnos=List_OTU_2b_removed_small.txt,constaxonomy=final.taxonomy_TEST)
[ERROR]: 00783122022122471063711866RAM used: 0.00453949Gigabytes . Total Ram: 754.39Gigabytes.

 has occurred in the Utils class function mothurConvert-int. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry

Is this a memory issue?
Thanks in advance

2

Can you post the first few lines of List_OTU_2b_removed_small.txt and final.taxonomy_TEST?

Pat

3

List_OTU_2b_removed_small.txt :
Otu00001
Otu00002
Otu00003
Otu00004
Otu00005
Otu00006
Otu00007
Otu00008
Otu00009
Otu00010

final.taxonomy_TEST:

A00783_1220_HTG2HDRX2_1_2213_25274_14982 Bacteria(100);Bacteria_unclassified(100);Bacteria_unclassified(100);Bacteria_unclassified(100);Bacteria_unclassified(100);Bacteria_unclassified(100);
A00783_1220_HTG2HDRX2_1_2247_10637_11866 Bacteria(100);Armatimonadetes(100);Chthonomonadetes(100);Chthonomonadales(100);Chthonomonadaceae(100);Chthonomonas_Armatimonadetes_gp3(100);
A00783_1220_HTG2HDRX2_1_2240_21811_27806 Bacteria(100);Firmicutes(100);Bacilli(100);Bacillales(100);Bacillaceae_1(97);Anoxybacillus(95);
A00783_1220_HTG2HDRX2_1_2155_16152_1689 Bacteria(100);Proteobacteria(99);Deltaproteobacteria(96);Deltaproteobacteria_unclassified(96);Deltaproteobacteria_unclassified(96);Deltaproteobacteria_unclassified(96);
A00783_1220_HTG2HDRX2_1_2249_28628_6637 Bacteria(100);Firmicutes(100);Erysipelotrichia(93);Erysipelotrichales(93);Erysipelotrichaceae(93);Turicibacter(93);
A00783_1220_HTG2HDRX2_1_2235_24957_20729 Bacteria(100);Bacteroidetes(96);Bacteroidia(92);Bacteroidales(92);Bacteroidales_unclassified(92);Bacteroidales_unclassified(92);
A00783_1220_HTG2HDRX2_1_2136_15022_27727 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(99);Gammaproteobacteria_unclassified(99);Gammaproteobacteria_unclassified(99);Gammaproteobacteria_unclassified(99);
A00783_1220_HTG2HDRX2_1_2145_15067_25113 Bacteria(100);Bacteroidetes(99);Bacteroidia(98);Bacteroidales(98);Porphyromonadaceae(94);Porphyromonadaceae_unclassified(94);
A00783_1220_HTG2HDRX2_1_2233_18783_20995 Bacteria(100);Firmicutes(80);Firmicutes_unclassified(80);Firmicutes_unclassified(80);Firmicutes_unclassified(80);Firmicutes_unclassified(80);
A00783_1220_HTG2HDRX2_1_2276_16947_25050 Bacteria(100);Cyanobacteria_Chloroplast(100);Chloroplast(100);Chloroplast_order_incertae_sedis(100);Chloroplast(100);Streptophyta(100);

Thank you.

4

It looks like your txt file has the names of OTUs you want to remove, but your taxonomy file has sequence names. The taxonomy you want should have originally had a name that ended in something like cons.taxonomy.

Pat

5

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