Attempting to add duplicate row

[liu-congcong]

Hello,

I annotated some bins with GTDB-TK v2.3.2 and always encountered this error.
Is there any parameter I can set to skip this error?

==> Running pplacer v1.1.alpha19-0-g807f6f3 analysis on gtdbtk-classify/classify/intermediate_results/pplacer/tree_1/user_msa_file.fasta.
==> Step 2 of 9: Pre-masking sequences.
[2024-03-08 10:52:54] INFO: Calculating RED values based on reference tree.
[2024-03-08 10:53:00] TASK: Traversing tree to determine classification method.
[2024-03-08 10:53:00] INFO: Completed 1 genome in 0.00 seconds (1,468.59 genomes/second).
[2024-03-08 10:53:00] TASK: Calculating average nucleotide identity using FastANI (v1.33).
[2024-03-08 10:53:07] INFO: Completed 36 comparisons in 6.71 seconds (5.37 comparisons/second).
[2024-03-08 10:53:08] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2024-03-08 10:53:09] ERROR: Attempting to add duplicate row: X01
[2024-03-08 10:53:09] ERROR: Controlled exit resulting from an unrecoverable error or warning.

[liu-congcong]

[liu-congcong]

To continue, I modified ClassifySummaryFile.add_row(), to report the gid when the error occurs.
Hopefully this bug will be fixed in a later update.

[pchaumeil]

Hello,
Thanks for the report.
Could you please send us a small input dataset generating this error so we can reproduce it on our end?
We will also need the command lines you are running

Thanks,
Pierre

[liu-congcong]

Hi,

The fasta file is:

X1.fasta.gz

The commands are:

FASTAPATH=/path/to/fastas/
THREADS=100
PPLACERTHREADS=2
GTDBMASH=/path/to/gtdb.msh
GTDBTK=gtdbtk

${GTDBTK} identify --extension fasta --cpus ${THREADS} --genome_dir ${FASTAPATH} --out_dir gtdbtk-identify
${GTDBTK} align --cpus ${THREADS} --identify_dir gtdbtk-identify --out_dir gtdbtk-align
${GTDBTK} classify --extension fasta --cpus ${THREADS} --pplacer_cpus ${PPLACERTHREADS} --genome_dir ${FASTAPATH} --align_dir gtdbtk-align --mash_db ${GTDBMASH} --out_dir gtdbtk-classify

And env is:

[2024-03-09 01:23:18] INFO: GTDB-Tk v2.3.2
[2024-03-09 01:23:18] INFO: gtdbtk check_install
[2024-03-09 01:23:18] INFO: Using GTDB-Tk reference data version r214: /path/to/gtdb-214
[2024-03-09 01:23:18] INFO: Running install verification
[2024-03-09 01:23:18] INFO: Checking that all third-party software are on the system path:
[2024-03-09 01:23:18] INFO: |-- FastTree OK
[2024-03-09 01:23:18] INFO: |-- FastTreeMP OK
[2024-03-09 01:23:18] INFO: |-- fastANI OK
[2024-03-09 01:23:18] INFO: |-- guppy OK
[2024-03-09 01:23:18] INFO: |-- hmmalign OK
[2024-03-09 01:23:18] INFO: |-- hmmsearch OK
[2024-03-09 01:23:18] INFO: |-- mash OK
[2024-03-09 01:23:18] INFO: |-- pplacer OK
[2024-03-09 01:23:18] INFO: |-- prodigal OK
[2024-03-09 01:23:18] INFO: Checking integrity of reference package: /path/to/gtdb-214
[2024-03-09 01:23:19] INFO: |-- pplacer OK
[2024-03-09 01:23:19] INFO: |-- masks OK
[2024-03-09 01:23:20] INFO: |-- markers OK
[2024-03-09 01:23:20] INFO: |-- radii OK
[2024-03-09 01:23:36] INFO: |-- msa OK
[2024-03-09 01:23:36] INFO: |-- metadata OK
[2024-03-09 01:23:36] INFO: |-- taxonomy OK

Best,
Cong-Cong