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