[2024-01-24 13:49:27,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,522] [INFO] DQC Reference Directory: /var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference
[2024-01-24 13:49:28,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,879] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,879] [INFO] Running command: gunzip -c /var/lib/cwl/stga671056c-a68f-4ed4-b6ec-d9adaced1887/GCF_002504165.1_ASM250416v1_genomic.fna.gz | prodigal -d GCF_002504165.1_ASM250416v1_genomic.fna/cds.fna -a GCF_002504165.1_ASM250416v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:41,889] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:41,889] [INFO] Task started: HMMsearch
[2024-01-24 13:49:41,890] [INFO] Running command: hmmsearch --tblout GCF_002504165.1_ASM250416v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference/reference_markers.hmm GCF_002504165.1_ASM250416v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,192] [INFO] Found 6/6 markers.
[2024-01-24 13:49:42,225] [INFO] Query marker FASTA was written to GCF_002504165.1_ASM250416v1_genomic.fna/markers.fasta
[2024-01-24 13:49:42,225] [INFO] Task started: Blastn
[2024-01-24 13:49:42,225] [INFO] Running command: blastn -query GCF_002504165.1_ASM250416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference/reference_markers.fasta -out GCF_002504165.1_ASM250416v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,185] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,188] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:43,188] [INFO] Target genome list was writen to GCF_002504165.1_ASM250416v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,194] [INFO] Task started: fastANI
[2024-01-24 13:49:43,195] [INFO] Running command: fastANI --query /var/lib/cwl/stga671056c-a68f-4ed4-b6ec-d9adaced1887/GCF_002504165.1_ASM250416v1_genomic.fna.gz --refList GCF_002504165.1_ASM250416v1_genomic.fna/target_genomes.txt --output GCF_002504165.1_ASM250416v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,178] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:04,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,179] [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
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	100.0	1314	1315	95	conclusive
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.0081	354	1315	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5669	508	1315	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.5031	383	1315	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.4471	377	1315	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.2621	358	1315	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.253	355	1315	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.2259	364	1315	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1926	354	1315	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.1793	384	1315	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.1759	359	1315	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.1404	358	1315	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.1327	430	1315	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.0964	361	1315	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.9954	379	1315	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.978	362	1315	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.9625	383	1315	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9481	365	1315	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.944	309	1315	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.906	324	1315	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	77.7553	339	1315	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	77.7067	297	1315	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.6396	337	1315	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.6338	337	1315	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.611	302	1315	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.6088	298	1315	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	76.9307	214	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,184] [INFO] DFAST Taxonomy check result was written to GCF_002504165.1_ASM250416v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference/checkm_data
[2024-01-24 13:50:04,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:04,234] [INFO] Task started: CheckM
[2024-01-24 13:50:04,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002504165.1_ASM250416v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002504165.1_ASM250416v1_genomic.fna/checkm_input GCF_002504165.1_ASM250416v1_genomic.fna/checkm_result
[2024-01-24 13:50:44,412] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:44,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:44,434] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:44,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:44,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002504165.1_ASM250416v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:44,435] [INFO] Task started: Blastn
[2024-01-24 13:50:44,435] [INFO] Running command: blastn -query GCF_002504165.1_ASM250416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0214ee-39dc-4564-b21f-1d1fb943d72a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002504165.1_ASM250416v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:46,174] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:46,178] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:46,179] [INFO] Target genome list was writen to GCF_002504165.1_ASM250416v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:46,213] [INFO] Task started: fastANI
[2024-01-24 13:50:46,213] [INFO] Running command: fastANI --query /var/lib/cwl/stga671056c-a68f-4ed4-b6ec-d9adaced1887/GCF_002504165.1_ASM250416v1_genomic.fna.gz --refList GCF_002504165.1_ASM250416v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002504165.1_ASM250416v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:06,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:06,629] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:06,629] [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_002504165.1	s__Pacificitalea manganoxidans	100.0	1315	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	conclusive
GCF_000152625.1	s__Roseovarius nubinhibens	78.9824	356	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.7809	366	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.6814	429	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.5722	506	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_001975705.1	s__Salipiger abyssi	78.514	457	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.5031	383	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017311415.1	s__Salipiger abyssi_A	78.3841	425	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	78.3682	384	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_009363255.1	s__Roseivivax sp009363255	78.3114	345	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.2318	357	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_008728195.1	s__Roseovarius indicus	78.18	360	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.1072	433	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	77.9157	323	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.8729	356	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.8288	357	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	77.721	328	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.7188	379	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006351965.1	s__Vannielia sp006351965	77.6908	344	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	77.6396	337	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	77.6325	391	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.6032	304	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCA_002706605.1	s__SAT37 sp002706605	77.5326	275	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.5268	419	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359745.1	s__JACIYW01 sp014359745	77.4355	270	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119405.1	s__Fluviibacterium sp002119405	77.1687	220	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:06,631] [INFO] GTDB search result was written to GCF_002504165.1_ASM250416v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:06,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:06,636] [INFO] DFAST_QC result json was written to GCF_002504165.1_ASM250416v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:06,637] [INFO] DFAST_QC completed!
[2024-01-24 13:51:06,637] [INFO] Total running time: 0h1m39s