[2024-01-24 13:18:41,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference
[2024-01-24 13:18:42,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,946] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,946] [INFO] Running command: gunzip -c /var/lib/cwl/stge1a00622-f6da-4ba1-8e31-fa5e7d228082/GCF_022488045.1_ASM2248804v1_genomic.fna.gz | prodigal -d GCF_022488045.1_ASM2248804v1_genomic.fna/cds.fna -a GCF_022488045.1_ASM2248804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:55,529] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:55,530] [INFO] Task started: HMMsearch
[2024-01-24 13:18:55,530] [INFO] Running command: hmmsearch --tblout GCF_022488045.1_ASM2248804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference/reference_markers.hmm GCF_022488045.1_ASM2248804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:55,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:55,828] [INFO] Found 6/6 markers.
[2024-01-24 13:18:55,868] [INFO] Query marker FASTA was written to GCF_022488045.1_ASM2248804v1_genomic.fna/markers.fasta
[2024-01-24 13:18:55,869] [INFO] Task started: Blastn
[2024-01-24 13:18:55,869] [INFO] Running command: blastn -query GCF_022488045.1_ASM2248804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference/reference_markers.fasta -out GCF_022488045.1_ASM2248804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:56,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:56,576] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:56,577] [INFO] Target genome list was writen to GCF_022488045.1_ASM2248804v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:56,587] [INFO] Task started: fastANI
[2024-01-24 13:18:56,587] [INFO] Running command: fastANI --query /var/lib/cwl/stge1a00622-f6da-4ba1-8e31-fa5e7d228082/GCF_022488045.1_ASM2248804v1_genomic.fna.gz --refList GCF_022488045.1_ASM2248804v1_genomic.fna/target_genomes.txt --output GCF_022488045.1_ASM2248804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:08,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:08,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:08,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:08,727] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:08,728] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:08,728] [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
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	86.3967	954	1240	95	below_threshold
Aestuariibaculum suncheonense	strain=SC17	GCA_014596935.1	1028745	1028745	type	True	85.0056	890	1240	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	80.8768	684	1240	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.5099	425	1240	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.3027	418	1240	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.3009	321	1240	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.0717	379	1240	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.9398	339	1240	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.8668	328	1240	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.8267	272	1240	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.8207	301	1240	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.7849	320	1240	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.7275	305	1240	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.5615	196	1240	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.4622	174	1240	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.3103	168	1240	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.2578	170	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,730] [INFO] DFAST Taxonomy check result was written to GCF_022488045.1_ASM2248804v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:08,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:08,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:08,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference/checkm_data
[2024-01-24 13:19:08,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:08,777] [INFO] Task started: CheckM
[2024-01-24 13:19:08,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022488045.1_ASM2248804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022488045.1_ASM2248804v1_genomic.fna/checkm_input GCF_022488045.1_ASM2248804v1_genomic.fna/checkm_result
[2024-01-24 13:19:47,980] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:47,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:48,006] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:48,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:48,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022488045.1_ASM2248804v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:48,008] [INFO] Task started: Blastn
[2024-01-24 13:19:48,008] [INFO] Running command: blastn -query GCF_022488045.1_ASM2248804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccaf42fe-f771-49fa-9f91-e6fe7fd10044/dqc_reference/reference_markers_gtdb.fasta -out GCF_022488045.1_ASM2248804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:49,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:49,099] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:49,099] [INFO] Target genome list was writen to GCF_022488045.1_ASM2248804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:49,143] [INFO] Task started: fastANI
[2024-01-24 13:19:49,143] [INFO] Running command: fastANI --query /var/lib/cwl/stge1a00622-f6da-4ba1-8e31-fa5e7d228082/GCF_022488045.1_ASM2248804v1_genomic.fna.gz --refList GCF_022488045.1_ASM2248804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022488045.1_ASM2248804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:58,729] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,744] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:58,744] [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_014596975.1	s__Aestuariibaculum marinum	86.3867	955	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596935.1	s__Aestuariibaculum suncheonense	85.0003	891	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596945.1	s__Aestuariibaculum sediminum	80.864	685	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	78.9355	422	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.7982	438	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.5129	424	1240	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	78.2625	380	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	78.0858	376	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.0503	369	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	78.0493	382	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.9235	342	1240	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_004791695.1	s__Flavivirga rizhaonensis	77.7784	322	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.4804	236	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,745] [INFO] GTDB search result was written to GCF_022488045.1_ASM2248804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:58,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:58,750] [INFO] DFAST_QC result json was written to GCF_022488045.1_ASM2248804v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:58,750] [INFO] DFAST_QC completed!
[2024-01-24 13:19:58,750] [INFO] Total running time: 0h1m17s