[2024-01-24 11:26:02,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:02,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:02,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference
[2024-01-24 11:26:04,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,144] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,144] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb2b37b4-22ef-4f45-8c50-193cd6b2a0a7/GCF_002893765.1_ASM289376v1_genomic.fna.gz | prodigal -d GCF_002893765.1_ASM289376v1_genomic.fna/cds.fna -a GCF_002893765.1_ASM289376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:17,511] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:17,511] [INFO] Task started: HMMsearch
[2024-01-24 11:26:17,511] [INFO] Running command: hmmsearch --tblout GCF_002893765.1_ASM289376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference/reference_markers.hmm GCF_002893765.1_ASM289376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:17,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:17,751] [INFO] Found 6/6 markers.
[2024-01-24 11:26:17,780] [INFO] Query marker FASTA was written to GCF_002893765.1_ASM289376v1_genomic.fna/markers.fasta
[2024-01-24 11:26:17,781] [INFO] Task started: Blastn
[2024-01-24 11:26:17,781] [INFO] Running command: blastn -query GCF_002893765.1_ASM289376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference/reference_markers.fasta -out GCF_002893765.1_ASM289376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:18,456] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:18,459] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:18,459] [INFO] Target genome list was writen to GCF_002893765.1_ASM289376v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:18,479] [INFO] Task started: fastANI
[2024-01-24 11:26:18,479] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb2b37b4-22ef-4f45-8c50-193cd6b2a0a7/GCF_002893765.1_ASM289376v1_genomic.fna.gz --refList GCF_002893765.1_ASM289376v1_genomic.fna/target_genomes.txt --output GCF_002893765.1_ASM289376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:33,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:33,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:33,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:33,491] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:33,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:33,491] [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
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	100.0	1371	1372	95	conclusive
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	90.7813	925	1372	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	81.3388	659	1372	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.6634	403	1372	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.6101	404	1372	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.5708	414	1372	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.5232	397	1372	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.4776	397	1372	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.3292	402	1372	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	78.3184	329	1372	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.1313	354	1372	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.0806	308	1372	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8959	327	1372	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.8939	333	1372	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.6699	258	1372	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.6644	264	1372	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.5843	249	1372	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.2755	198	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:33,493] [INFO] DFAST Taxonomy check result was written to GCF_002893765.1_ASM289376v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:33,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:33,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:33,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference/checkm_data
[2024-01-24 11:26:33,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:33,535] [INFO] Task started: CheckM
[2024-01-24 11:26:33,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002893765.1_ASM289376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002893765.1_ASM289376v1_genomic.fna/checkm_input GCF_002893765.1_ASM289376v1_genomic.fna/checkm_result
[2024-01-24 11:27:14,021] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:14,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,039] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:14,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:14,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002893765.1_ASM289376v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:14,040] [INFO] Task started: Blastn
[2024-01-24 11:27:14,040] [INFO] Running command: blastn -query GCF_002893765.1_ASM289376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5628de54-e80d-4a46-a472-e02ccc74f1d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002893765.1_ASM289376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,971] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,974] [INFO] Selected 7 target genomes.
[2024-01-24 11:27:14,974] [INFO] Target genome list was writen to GCF_002893765.1_ASM289376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:14,979] [INFO] Task started: fastANI
[2024-01-24 11:27:14,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb2b37b4-22ef-4f45-8c50-193cd6b2a0a7/GCF_002893765.1_ASM289376v1_genomic.fna.gz --refList GCF_002893765.1_ASM289376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002893765.1_ASM289376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:22,817] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:22,825] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:22,825] [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_002893765.1	s__Tamlana_A carrageenivorans	100.0	1371	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001642835.1	s__Tamlana_A agarivorans	90.775	926	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_015355625.1	s__Tamlana_A sp015355625	83.951	770	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	81.3216	661	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	80.7939	713	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	78.3706	331	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	77.6432	261	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:22,826] [INFO] GTDB search result was written to GCF_002893765.1_ASM289376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:22,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:22,831] [INFO] DFAST_QC result json was written to GCF_002893765.1_ASM289376v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:22,831] [INFO] DFAST_QC completed!
[2024-01-24 11:27:22,831] [INFO] Total running time: 0h1m20s