ERROR: DIAMOND finished abnormally

[jiaojiaoguan]

hi,
when I run the command ./CAT_pack/CAT contigs -c "/home/jiaojiao/cat/test.fasta" -d /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/ -t /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/ --verbose

there is a error. ERROR: DIAMOND finished abnormally. The diamond version is correct. And I set the tmpdir. So I do not know how to fix it.

The detailed output file is like this:

` # CAT v5.2.3.

CAT is running. Protein prediction, alignment, and contig classification are carried out.
Rarw!

Supplied command: ./CAT_pack/CAT contigs -c /home/jiaojiao/cat/test.fasta -d /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/ -t /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/ --verbose

Contigs fasta: /home/jiaojiao/cat/test.fasta
Taxonomy folder: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/
Database folder: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/
Parameter r: 10
Parameter f: 0.5
Log file: ./out.CAT.log

---

Doing some pre-flight checks first.
[2022-06-23 20:19:01] Prodigal found: Prodigal V2.6.3: February, 2016.
[2022-06-23 20:19:01] DIAMOND found: diamond version 2.0.6.

---

Full list of arguments:
IkwId: False
ORF2LCA_output_file: ./out.CAT.ORF2LCA.txt
alignment_file: ./out.CAT.alignment.diamond
block_size: 2.0
compress: False
contig2classification_output_file: ./out.CAT.contig2classification.txt
contigs_fasta: /home/jiaojiao/cat/test.fasta
database_folder: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/
db_fasta: None
diamond_database: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/2021-01-07.nr.dmnd
f: 0.5
fastaid2LCAtaxid_file: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/2021-01-07.nr.fastaid2LCAtaxid
force: False
index_chunks: 4
log_file: ./out.CAT.log
names_dmp: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/names.dmp
no_log: False
no_self_hits: False
no_stars: False
nodes_dmp: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/nodes.dmp
nproc: 2
one_minus_r: 0.9
out_prefix: ./out.CAT
path_to_diamond: diamond
path_to_prodigal: prodigal
prot_accession2taxid_file: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/2021-01-07.prot.accession2taxid.FULL.gz
proteins_fasta: ./out.CAT.predicted_proteins.faa
proteins_gff: ./out.CAT.predicted_proteins.gff
quiet: False
r: 10
sensitive: False
taxids_with_multiple_offspring_file: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/2021-01-07.nr.taxids_with_multiple_offspring
taxonomy_folder: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_taxonomy/
tmpdir: /home/jiaojiao/cat/CAT-master/log/
top: 50
verbose: True

Step list: ['predict_proteins', 'align', 'classify']

---

Ready to fly!

---

[2022-06-23 20:19:01] Importing contig names from /home/jiaojiao/cat/test.fasta.
[2022-06-23 20:19:01] Running Prodigal for ORF prediction. Files ./out.CAT.predicted_proteins.faa and ./out.CAT.predicted_proteins.gff will be generated. Do not forget to cite Prodigal when using CAT or BAT in your publication.
[2022-06-23 20:22:34] ORF prediction done!
[2022-06-23 20:22:34] Parsing ORF file ./out.CAT.predicted_proteins.faa
[2022-06-23 20:22:34] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication.
query: ./out.CAT.predicted_proteins.faa
database: /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/2021-01-07.nr.dmnd
mode: fast
top: 50
no-self-hits: False
number of cores: 2
block-size (billions of letters): 2.0
index-chunks: 4
tmpdir: /home/jiaojiao/cat/CAT-master/log/
compress: 0
diamond v2.0.6.144 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 2
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /home/jiaojiao/cat/CAT-master/log/
Opening the database... [0.701s]
Percentage range of top alignment score to report hits: 50
Reference = /home/jiaojiao/cat/CAT_prepare_20210107/2021-01-07_CAT_database/2021-01-07.nr.dmnd
Sequences = 338965036
Letters = 122594075914
Block size = 2000000000
Opening the input file... [0.014s]
Opening the output file... [0s]
Loading query sequences... [0.099s]
Masking queries... [0.615s]
Building query seed set... [0.076s]
Algorithm: Double-indexed
Building query histograms... [0.165s]
Allocating buffers... [0s]
Loading reference sequences... [31.767s]
Masking reference... [98.739s]
Initializing temporary storage... [0.002s]
Building reference histograms... [46.232s]
Allocating buffers... [0s]
Processing query block 1, reference block 1/62, shape 1/2, index chunk 1/4.
Building reference seed array... [2022-06-23 20:26:38] ERROR: DIAMOND finished abnormally.`

did you have some idea about it ?

Thank you！

[mihinduk]

I just ran into the same exact issue - 43 samples finished and 9 keep dying like this. Any suggestions?

[sean-workman]

Trying to resurrect this as I am also having problems with Diamond giving ERROR: DIAMOND finished abnormally.

Did anybody have any luck getting to the bottom of this?

[Elle-ctricity]

In case anyone encounters this error, I was able to successfully run CAT by updating the DIAMOND database to the latest, setting a --tmp directory to a directory with a lot of storage, and giving my system 60GB on memory in a pseudo-terminal. I am running this on a cluster