[2024-01-24 14:05:14,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:14,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:14,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference
[2024-01-24 14:05:15,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:15,213] [INFO] Task started: Prodigal
[2024-01-24 14:05:15,213] [INFO] Running command: gunzip -c /var/lib/cwl/stgc66ceddf-ff72-4080-af0d-651e6a81d6ea/GCF_017592335.1_ASM1759233v1_genomic.fna.gz | prodigal -d GCF_017592335.1_ASM1759233v1_genomic.fna/cds.fna -a GCF_017592335.1_ASM1759233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:26,556] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:26,557] [INFO] Task started: HMMsearch
[2024-01-24 14:05:26,557] [INFO] Running command: hmmsearch --tblout GCF_017592335.1_ASM1759233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference/reference_markers.hmm GCF_017592335.1_ASM1759233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:26,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:26,817] [INFO] Found 6/6 markers.
[2024-01-24 14:05:26,859] [INFO] Query marker FASTA was written to GCF_017592335.1_ASM1759233v1_genomic.fna/markers.fasta
[2024-01-24 14:05:26,860] [INFO] Task started: Blastn
[2024-01-24 14:05:26,860] [INFO] Running command: blastn -query GCF_017592335.1_ASM1759233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference/reference_markers.fasta -out GCF_017592335.1_ASM1759233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:27,690] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:27,695] [INFO] Selected 33 target genomes.
[2024-01-24 14:05:27,696] [INFO] Target genome list was writen to GCF_017592335.1_ASM1759233v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:27,737] [INFO] Task started: fastANI
[2024-01-24 14:05:27,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgc66ceddf-ff72-4080-af0d-651e6a81d6ea/GCF_017592335.1_ASM1759233v1_genomic.fna.gz --refList GCF_017592335.1_ASM1759233v1_genomic.fna/target_genomes.txt --output GCF_017592335.1_ASM1759233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:47,564] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:47,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:47,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:47,592] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:47,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:47,592] [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
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	77.4559	185	1253	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4024	231	1253	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.3588	275	1253	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.3457	176	1253	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.2614	227	1253	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.1968	223	1253	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.1824	235	1253	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.1766	234	1253	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.1584	170	1253	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.1132	226	1253	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.1059	172	1253	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.0999	217	1253	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.0784	175	1253	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.0694	213	1253	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.0589	171	1253	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.0365	234	1253	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.0346	164	1253	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	77.0103	153	1253	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.0097	231	1253	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	77.0067	136	1253	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.9798	174	1253	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	76.9684	153	1253	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.9292	190	1253	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.926	179	1253	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	76.8836	191	1253	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.8716	176	1253	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.8536	177	1253	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.7865	180	1253	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	76.783	160	1253	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7481	191	1253	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.7024	183	1253	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.5813	176	1253	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.3738	117	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:47,594] [INFO] DFAST Taxonomy check result was written to GCF_017592335.1_ASM1759233v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:47,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:47,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:47,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference/checkm_data
[2024-01-24 14:05:47,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:47,642] [INFO] Task started: CheckM
[2024-01-24 14:05:47,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017592335.1_ASM1759233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017592335.1_ASM1759233v1_genomic.fna/checkm_input GCF_017592335.1_ASM1759233v1_genomic.fna/checkm_result
[2024-01-24 14:06:26,318] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:26,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,348] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:26,348] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:26,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017592335.1_ASM1759233v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:26,349] [INFO] Task started: Blastn
[2024-01-24 14:06:26,349] [INFO] Running command: blastn -query GCF_017592335.1_ASM1759233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b9c6100-aaf4-42a0-b7ba-1adc7aa5d996/dqc_reference/reference_markers_gtdb.fasta -out GCF_017592335.1_ASM1759233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:27,915] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:27,918] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:27,918] [INFO] Target genome list was writen to GCF_017592335.1_ASM1759233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:27,942] [INFO] Task started: fastANI
[2024-01-24 14:06:27,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgc66ceddf-ff72-4080-af0d-651e6a81d6ea/GCF_017592335.1_ASM1759233v1_genomic.fna.gz --refList GCF_017592335.1_ASM1759233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017592335.1_ASM1759233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:54,278] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:54,301] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:54,301] [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_017592335.1	s__Sulfitobacter_F sp017592335	100.0	1247	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013315265.1	s__Sulfitobacter_F algicola	82.1115	445	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	77.8264	302	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.4885	222	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.4604	249	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_009857745.1	s__Thalassobius mangrovi	77.3953	231	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.3695	274	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000671395.1	s__Actibacterium atlanticum	77.3353	176	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.2125	240	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.1938	234	1253	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_900142185.1	s__Lutimaribacter pacificus	77.178	242	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005938225.1	s__Arenibacterium halophilum	77.1629	243	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.1611	254	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743975.1	s__Ruegeria sp017743975	77.1349	186	1253	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	77.103	227	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.0587	214	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	77.0572	184	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.0303	244	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	77.0097	231	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_900172335.1	s__Roseovarius albus	76.9933	136	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	76.89	203	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	76.881	167	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	76.7001	124	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	76.6927	174	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654855.1	s__JAATGA01 sp015654855	76.0458	83	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAATGA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,303] [INFO] GTDB search result was written to GCF_017592335.1_ASM1759233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:54,303] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:54,308] [INFO] DFAST_QC result json was written to GCF_017592335.1_ASM1759233v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:54,308] [INFO] DFAST_QC completed!
[2024-01-24 14:06:54,308] [INFO] Total running time: 0h1m40s