[2024-01-24 13:45:58,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:58,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:58,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference
[2024-01-24 13:46:00,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,241] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg9734441a-bc44-4932-8659-93f42665c298/GCF_031932625.1_ASM3193262v1_genomic.fna.gz | prodigal -d GCF_031932625.1_ASM3193262v1_genomic.fna/cds.fna -a GCF_031932625.1_ASM3193262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:15,519] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:15,520] [INFO] Task started: HMMsearch
[2024-01-24 13:46:15,520] [INFO] Running command: hmmsearch --tblout GCF_031932625.1_ASM3193262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference/reference_markers.hmm GCF_031932625.1_ASM3193262v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:15,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:15,829] [INFO] Found 6/6 markers.
[2024-01-24 13:46:15,864] [INFO] Query marker FASTA was written to GCF_031932625.1_ASM3193262v1_genomic.fna/markers.fasta
[2024-01-24 13:46:15,864] [INFO] Task started: Blastn
[2024-01-24 13:46:15,865] [INFO] Running command: blastn -query GCF_031932625.1_ASM3193262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference/reference_markers.fasta -out GCF_031932625.1_ASM3193262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:16,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:16,611] [INFO] Selected 23 target genomes.
[2024-01-24 13:46:16,612] [INFO] Target genome list was writen to GCF_031932625.1_ASM3193262v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:16,643] [INFO] Task started: fastANI
[2024-01-24 13:46:16,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg9734441a-bc44-4932-8659-93f42665c298/GCF_031932625.1_ASM3193262v1_genomic.fna.gz --refList GCF_031932625.1_ASM3193262v1_genomic.fna/target_genomes.txt --output GCF_031932625.1_ASM3193262v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:35,482] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:35,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:35,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:35,501] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:35,501] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:35,501] [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
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.568	452	1246	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.3778	394	1246	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.3361	393	1246	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.3225	420	1246	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.3157	419	1246	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.3074	420	1246	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.2236	419	1246	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.2088	420	1246	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	78.1709	368	1246	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.1666	424	1246	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	78.1435	300	1246	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	78.116	363	1246	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.0845	380	1246	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.0707	368	1246	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	78.0538	369	1246	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.0309	360	1246	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.0053	367	1246	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.8763	349	1246	95	below_threshold
Mariniflexile maritimum	strain=M5A1M	GCA_009746565.1	2682493	2682493	type	True	77.8722	368	1246	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.596	352	1246	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.4636	274	1246	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4259	220	1246	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4033	227	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:35,503] [INFO] DFAST Taxonomy check result was written to GCF_031932625.1_ASM3193262v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:35,504] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:35,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:35,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference/checkm_data
[2024-01-24 13:46:35,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:35,552] [INFO] Task started: CheckM
[2024-01-24 13:46:35,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031932625.1_ASM3193262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031932625.1_ASM3193262v1_genomic.fna/checkm_input GCF_031932625.1_ASM3193262v1_genomic.fna/checkm_result
[2024-01-24 13:47:22,591] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:22,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:22,616] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:22,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:22,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031932625.1_ASM3193262v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:22,618] [INFO] Task started: Blastn
[2024-01-24 13:47:22,618] [INFO] Running command: blastn -query GCF_031932625.1_ASM3193262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c2de3c8-0053-4f24-a522-1cde1482e348/dqc_reference/reference_markers_gtdb.fasta -out GCF_031932625.1_ASM3193262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:23,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:23,541] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:23,541] [INFO] Target genome list was writen to GCF_031932625.1_ASM3193262v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:23,566] [INFO] Task started: fastANI
[2024-01-24 13:47:23,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg9734441a-bc44-4932-8659-93f42665c298/GCF_031932625.1_ASM3193262v1_genomic.fna.gz --refList GCF_031932625.1_ASM3193262v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031932625.1_ASM3193262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:37,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:37,029] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:37,030] [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_000789235.1	s__Wocania ichthyoenteri	82.4287	806	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	79.9719	652	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498295.1	s__Wocania sp009498295	78.8345	483	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.5675	452	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.5413	441	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.369	396	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.3359	393	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.3225	419	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900141715.1	s__Arenitalea lutea	78.2085	422	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.0936	379	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	78.062	369	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943555.1	s__Tamlana_B nanhaiensis	78.04	372	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	78.0312	360	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_008033385.1	s__Algibacter pacificus	78.0218	364	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111025.1	s__Jejuia jejuensis	77.9887	300	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	77.9231	354	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.9216	307	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.6075	350	1246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,036] [INFO] GTDB search result was written to GCF_031932625.1_ASM3193262v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:37,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:37,040] [INFO] DFAST_QC result json was written to GCF_031932625.1_ASM3193262v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:37,040] [INFO] DFAST_QC completed!
[2024-01-24 13:47:37,041] [INFO] Total running time: 0h1m38s