Weird problem of the blast algorithm with assign_taxonomy.py

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Chih

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Jan 4, 2019, 11:39:05 AM1/4/19
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Dear Qiime 1 users:

I got a weird result from using assign_taxonomy.py with the function -m blast.
Basically, the command worked and generated the log file as output file. The information in the log file is:

-------
lastTaxonAssigner parameters:
Application:blastn/megablast
Max E value:0.001
Min percent identity:90.0
id_to_taxonomy_filepath:/path/developer/sh_taxonomy_qiime_ver7_97_01.12.2017_dev.txt
reference_seqs_filepath:/path/developer/sh_refs_qiime_ver7_97_01.12.2017_dev.fasta
Number of sequences inspected: 75
Number with no blast hits: 75
Result path: /tmp/assign-tax3xRia6
---------
And nothing afterwards.

Thus, I think the incorporation of the qiime1 with blast might have some problems, but I cannot find what might be the reason for that.

However, if I used the same command (without indicating -m blast) by using the default algorithm, uclust, with exactly the same command. The log file is:

-------
UclustConsensusTaxonAssigner parameters:
id_to_taxonomy_filepath:/path/developer/sh_taxonomy_qiime_ver7_97_01.12.2017_dev.txt
id_to_taxonomy_fp:/path/developer/sh_taxonomy_qiime_ver7_97_01.12.2017_dev.txt
max_accepts:3
min_consensus_fraction:0.51
reference_sequences_fp:/path/developer/sh_refs_qiime_ver7_97_01.12.2017_dev.fasta
similarity:0.9
unassignable_label:Unassigned
Result path: /tmp/assign-taxPD_n9w

.uc file contents:

# uclust --input /path/data.fa --id 0.9 --rev --maxaccepts 3 --allhits --libonly --lib /path/developer/sh_refs_qiime_ver7_97_01.12.2017_dev.fasta --uc /tmp/UclustConsensusTaxonAssigner_DSfjiT.uc
# version=1.2.22
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
L 7293 716 * * * * * SH494153.07FU_HG935852_reps *
H 7293 257 93.4 + 0 0 10I211MI30MD15M449I OTU8.17739595034258e+28 SH494153.07FU_HG935852_reps
L 9750 658 * * * * * SH0354.07FU_AY046553_refs *
H 9750 257 92.2 + 0 0 37MI77MI74MD68M400I OTU8.17739595034258e+28 SH0354.07FU_AY046553_refs
L 19700 720 * * * * * SH006345.07FU_KF057516_reps *
H 19700 257 91.4 + 0 0 16I26MI11M3I46MI35M4I70MD54MI14M438I OTU8.17739595034258e+28 SH006345.07FU_KF057516_reps
L 5173 1137 * * * * * SH017876.07FU_JN890081_reps *
H 5173 182 97.3 + 0 0 6I87MI74MI21M947I OTU9.15302265991585e+28 SH017876.07FU_JN890081_reps
H 5173 181 97.2 + 0 0 6I11MI74MI76MI20M947I OTU9.90187917408672e+28 SH017876.07FU_JN890081_reps
H 5173 181 96.7 + 0 0 6I11MI74MI76MI20M947I OTU2.34003445922049e+28 SH017876.07FU_JN890081_reps
-------
(There are still many lines behind with similar formats)

Could anyone help me to figure out why they made such a difference?

Thank you.

Chih

Lynn

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Dec 1, 2019, 7:05:29 AM12/1/19
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Hi, I am also facing problem like you. How do you solve it? I cannot install blast in my miniconda. So, I use default uclust. I am also analyzing for cbbM, functional gene for oxidase enzyme. If you know how to solve problem, please help me. thank u so much.
lynn

Colin Brislawn

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Dec 5, 2019, 3:35:44 PM12/5/19
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Good afternoon,

I wonder if legacy blast (not blast+) is being installed correctly by conda. I know this has been an issue in the past and this would explain why uclust but not blast is working. 

Colin

Lynn

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Dec 6, 2019, 1:53:39 AM12/6/19
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Dear Colin,
Thanks for your answer.
 I did not install legacy, only blast+. I don't know how to install it.
tar zxvpf ncbi-blast-2.9.0+-x64-linux.tar.gz
export PATH=$PATH:$HOME/ncbi-blast-2.9.0+/bin
mkdir blastdb
export PATH=$PATH:$HOME/dell/miniconda3/wjs/ncbi-blast-2.9.0+/bin
rm ~/.ncbirc
export BLASTDB=~/home/wjs/blastdb
export BLASTMAT=~/home/wjs/blast-2.9.0/data 
I don't know what are these. But, I follow these commands and now, I can use blast in qiime. 
How to install legacy?
with best regards
lynn


Colin Brislawn

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Dec 6, 2019, 9:34:12 AM12/6/19
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Hello Lynn,

You can install the old blast using conda: 

I'm not sure if you need 2.2.22 or 2.2.26 of blast-legacy. Try both and see which one Qiime likes.

Or, upgrade to Qiime 2!

Colin

Lynn

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Dec 8, 2019, 4:08:04 AM12/8/19
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Thank you so much, Colin. I will install it.
best regards
lynn
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