[2024-01-24 11:12:39,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference
[2024-01-24 11:12:40,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,908] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg078669b1-67f0-442b-9262-c62d71ac2f44/GCF_016595505.1_ASM1659550v1_genomic.fna.gz | prodigal -d GCF_016595505.1_ASM1659550v1_genomic.fna/cds.fna -a GCF_016595505.1_ASM1659550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:20,181] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:20,182] [INFO] Task started: HMMsearch
[2024-01-24 11:13:20,182] [INFO] Running command: hmmsearch --tblout GCF_016595505.1_ASM1659550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference/reference_markers.hmm GCF_016595505.1_ASM1659550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:20,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:20,552] [INFO] Found 6/6 markers.
[2024-01-24 11:13:20,615] [INFO] Query marker FASTA was written to GCF_016595505.1_ASM1659550v1_genomic.fna/markers.fasta
[2024-01-24 11:13:20,616] [INFO] Task started: Blastn
[2024-01-24 11:13:20,616] [INFO] Running command: blastn -query GCF_016595505.1_ASM1659550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference/reference_markers.fasta -out GCF_016595505.1_ASM1659550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:21,293] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:21,298] [INFO] Selected 21 target genomes.
[2024-01-24 11:13:21,298] [INFO] Target genome list was writen to GCF_016595505.1_ASM1659550v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:21,306] [INFO] Task started: fastANI
[2024-01-24 11:13:21,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg078669b1-67f0-442b-9262-c62d71ac2f44/GCF_016595505.1_ASM1659550v1_genomic.fna.gz --refList GCF_016595505.1_ASM1659550v1_genomic.fna/target_genomes.txt --output GCF_016595505.1_ASM1659550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:40,061] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:40,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:40,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:40,073] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:40,073] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:40,074] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pelagicoccus mobilis	strain=KCTC 13126	GCA_016595505.1	415221	415221	type	True	100.0	2417	2423	95	conclusive
Pelagicoccus enzymogenes	strain=NFK12	GCA_014803405.1	2773457	2773457	type	True	79.4866	555	2423	95	below_threshold
Pelagicoccus albus	strain=JCM23202	GCA_014230145.1	415222	415222	type	True	78.4372	326	2423	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	75.9507	71	2423	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	75.762	57	2423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:40,076] [INFO] DFAST Taxonomy check result was written to GCF_016595505.1_ASM1659550v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:40,076] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:40,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:40,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference/checkm_data
[2024-01-24 11:13:40,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:40,145] [INFO] Task started: CheckM
[2024-01-24 11:13:40,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595505.1_ASM1659550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595505.1_ASM1659550v1_genomic.fna/checkm_input GCF_016595505.1_ASM1659550v1_genomic.fna/checkm_result
[2024-01-24 11:15:23,953] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:23,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:23,980] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:23,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:23,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595505.1_ASM1659550v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:23,981] [INFO] Task started: Blastn
[2024-01-24 11:15:23,981] [INFO] Running command: blastn -query GCF_016595505.1_ASM1659550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ca305de-8547-4709-b65c-0a31883b24ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595505.1_ASM1659550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:25,032] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:25,036] [INFO] Selected 17 target genomes.
[2024-01-24 11:15:25,036] [INFO] Target genome list was writen to GCF_016595505.1_ASM1659550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:25,051] [INFO] Task started: fastANI
[2024-01-24 11:15:25,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg078669b1-67f0-442b-9262-c62d71ac2f44/GCF_016595505.1_ASM1659550v1_genomic.fna.gz --refList GCF_016595505.1_ASM1659550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595505.1_ASM1659550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:39,053] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:39,059] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:39,059] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_016595505.1	s__Pelagicoccus mobilis	100.0	2417	2423	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000155695.1	s__Pelagicoccus sp000155695	79.5549	538	2423	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014803405.1	s__Pelagicoccus sp014803405	79.4961	554	2423	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230145.1	s__Pelagicoccus albus	78.4372	326	2423	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700525.1	s__UBA5691 sp018700525	76.4562	93	2423	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:39,060] [INFO] GTDB search result was written to GCF_016595505.1_ASM1659550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:39,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:39,063] [INFO] DFAST_QC result json was written to GCF_016595505.1_ASM1659550v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:39,063] [INFO] DFAST_QC completed!
[2024-01-24 11:15:39,064] [INFO] Total running time: 0h2m60s