[2024-01-24 13:21:47,034] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference
[2024-01-24 13:21:48,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,412] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,412] [INFO] Running command: gunzip -c /var/lib/cwl/stgbafaab1c-60a0-4b8b-b55d-d3eea52e3fd2/GCF_005938225.1_ASM593822v1_genomic.fna.gz | prodigal -d GCF_005938225.1_ASM593822v1_genomic.fna/cds.fna -a GCF_005938225.1_ASM593822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:03,789] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:03,790] [INFO] Task started: HMMsearch
[2024-01-24 13:22:03,790] [INFO] Running command: hmmsearch --tblout GCF_005938225.1_ASM593822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference/reference_markers.hmm GCF_005938225.1_ASM593822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:04,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:04,095] [INFO] Found 6/6 markers.
[2024-01-24 13:22:04,135] [INFO] Query marker FASTA was written to GCF_005938225.1_ASM593822v1_genomic.fna/markers.fasta
[2024-01-24 13:22:04,135] [INFO] Task started: Blastn
[2024-01-24 13:22:04,136] [INFO] Running command: blastn -query GCF_005938225.1_ASM593822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference/reference_markers.fasta -out GCF_005938225.1_ASM593822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:05,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:05,085] [INFO] Selected 29 target genomes.
[2024-01-24 13:22:05,086] [INFO] Target genome list was writen to GCF_005938225.1_ASM593822v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:05,155] [INFO] Task started: fastANI
[2024-01-24 13:22:05,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafaab1c-60a0-4b8b-b55d-d3eea52e3fd2/GCF_005938225.1_ASM593822v1_genomic.fna.gz --refList GCF_005938225.1_ASM593822v1_genomic.fna/target_genomes.txt --output GCF_005938225.1_ASM593822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:28,408] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:28,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:28,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:28,432] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:28,433] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:28,433] [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
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.4548	634	1535	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.4521	552	1535	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.3771	513	1535	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.3137	604	1535	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.0813	540	1535	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.9345	558	1535	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.9023	503	1535	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.8695	555	1535	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	78.8542	534	1535	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	78.7976	520	1535	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.7932	551	1535	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	78.7711	587	1535	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.7139	535	1535	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.6367	536	1535	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.4961	488	1535	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.3937	519	1535	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.2339	402	1535	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.0871	471	1535	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	78.0849	449	1535	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.9132	361	1535	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8781	371	1535	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.7671	376	1535	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7087	362	1535	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.7066	354	1535	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.6635	418	1535	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6059	335	1535	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.5859	316	1535	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4261	346	1535	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.3247	354	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:28,435] [INFO] DFAST Taxonomy check result was written to GCF_005938225.1_ASM593822v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:28,436] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:28,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:28,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference/checkm_data
[2024-01-24 13:22:28,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:28,485] [INFO] Task started: CheckM
[2024-01-24 13:22:28,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005938225.1_ASM593822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005938225.1_ASM593822v1_genomic.fna/checkm_input GCF_005938225.1_ASM593822v1_genomic.fna/checkm_result
[2024-01-24 13:23:18,867] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:18,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:18,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:18,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:18,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005938225.1_ASM593822v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:18,887] [INFO] Task started: Blastn
[2024-01-24 13:23:18,888] [INFO] Running command: blastn -query GCF_005938225.1_ASM593822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39ab4ad9-ecfa-4eb7-8dc2-208f33491a6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005938225.1_ASM593822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:20,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:20,489] [INFO] Selected 25 target genomes.
[2024-01-24 13:23:20,489] [INFO] Target genome list was writen to GCF_005938225.1_ASM593822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:20,501] [INFO] Task started: fastANI
[2024-01-24 13:23:20,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafaab1c-60a0-4b8b-b55d-d3eea52e3fd2/GCF_005938225.1_ASM593822v1_genomic.fna.gz --refList GCF_005938225.1_ASM593822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005938225.1_ASM593822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:42,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:42,723] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:42,723] [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_005938225.1	s__Arenibacterium halophilum	100.0	1535	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	conclusive
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.4417	679	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	79.7259	716	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.6096	570	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002210165.1	s__CAU-1492 sp002210165	79.5034	674	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	79.4791	549	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.4581	634	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.3669	525	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900109035.1	s__Cribrihabitans marinus	79.3442	574	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.3138	604	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_002210095.1	s__Marinibacterium profundimaris	79.2035	602	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	79.1441	654	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900108275.1	s__Jhaorihella thermophila	79.0327	542	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.982	509	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.9261	559	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.9022	503	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.8812	555	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.847	484	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCA_003511785.1	s__UBA7951 sp003511785	78.8284	385	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.77	571	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.6957	540	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	78.5042	487	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.1223	435	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.674	416	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_013282155.1	s__Sulfitobacter sp013282155	77.6049	359	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:42,725] [INFO] GTDB search result was written to GCF_005938225.1_ASM593822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:42,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:42,733] [INFO] DFAST_QC result json was written to GCF_005938225.1_ASM593822v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:42,733] [INFO] DFAST_QC completed!
[2024-01-24 13:23:42,733] [INFO] Total running time: 0h1m56s