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Error when run quick start
I was learning amptk, and ran AMPtk Quick Start guidling to process test data from and I got this error when filtering.
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Traceback (most recent call last):
File "/home/user1/miniconda3/envs/amptk154/bin/amptk", line 10, in filt2 = filtered.loc[(filtered != 0).any(1)]
to
filt2 = filtered.loc[(filtered != 0).any(axis=1)]
then the filter was run successfully.
but, when I ran amptk taxonomy after LULU, I get another problem,
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[03:51:57 PM]: OS: Ubuntu 20.04, 8 cores, ~ 25 GB RAM. Python: 3.8.18
[03:51:57 PM]: AMPtk v1.5.4, VSEARCH v2.24.0
[03:51:57 PM]: Loading FASTA Records
[03:51:57 PM]: 5 OTUs
[03:51:57 PM]: Global alignment OTUs with usearch_global (VSEARCH) against ITS.udb
[03:51:57 PM]: Classifying OTUs with SINTAX (VSEARCH)
[03:51:57 PM]: SINTAX results empty
[03:51:57 PM]: Parsing taxonomy failed -- see logfile
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there are no output result!!!
I checked log file. It shows below:
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[11/02/23 15:51:56]: /home/user1/miniconda3/envs/amptk154/bin/amptk taxonomy -f miseq.lulu.otus.fa -i miseq.lulu.otu_table.txt -m miseq.mapping_file.txt -d ITS2 -o miseq
[11/02/23 15:51:57]: OS: Ubuntu 20.04, 8 cores, ~ 25 GB RAM. Python: 3.8.18 [11/02/23 15:51:57]: Python Modules: numpy v1.24.4, pandas v2.0.3, matplotlib v3.4.3, psutil v5.9.5, natsort v8.4.0, biopython v1.81, edlib v1.3.9, biom-format v2.1.15 [11/02/23 15:51:57]: AMPtk v1.5.4, VSEARCH v2.24.0 [11/02/23 15:51:57]: Loading FASTA Records [11/02/23 15:51:57]: 5 OTUs [11/02/23 15:51:57]: Global alignment OTUs with usearch_global (VSEARCH) against ITS.udb [11/02/23 15:51:57]: vsearch --usearch_global miseq.lulu.otus.fa --db /home/user1/miniconda3/envs/amptk154/lib/python3.8/site-packages/amptk/DB/ITS.udb --userout miseq.usearch.txt --id 0.7 --strand both --output_no_hits --maxaccepts 500 --top_hits_only --userfields query+target+id --notrunclabels --threads 8 [11/02/23 15:51:57]: vsearch v2.24.0_linux_x86_64, 23.9GB RAM, 8 cores https://github.com/torognes/vsearch
Fatal error: Unable to get status for input file (/home/user1/miniconda3/envs/amptk154/lib/python3.8/site-packages/amptk/DB/ITS.udb)
[11/02/23 15:51:57]: Classifying OTUs with SINTAX (VSEARCH) [11/02/23 15:51:57]: vsearch --sintax miseq.lulu.otus.fa --db /home/user1/miniconda3/envs/amptk154/lib/python3.8/site-packages/amptk/DB/ITS2_SINTAX.udb --tabbedout miseq.sintax.txt -sintax_cutoff 0.8 --threads 8 --notrunclabels [11/02/23 15:51:57]: vsearch v2.24.0_linux_x86_64, 23.9GB RAM, 8 cores https://github.com/torognes/vsearch
Fatal error: Unable to get status for input file (/home/user1/miniconda3/envs/amptk154/lib/python3.8/site-packages/amptk/DB/ITS2_SINTAX.udb)
[11/02/23 15:51:57]: SINTAX results empty [11/02/23 15:51:57]: Global alignment results parsed, resulting in 0 taxonomy predictions [11/02/23 15:51:57]: Combined OTU taxonomy dictionary contains 0 taxonomy predictions [11/02/23 15:51:57]: Parsing taxonomy failed -- see logfile` ################ sameerror was also occur when I ran with amptk V 1.5.5