[2024-01-24 14:54:49,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference
[2024-01-24 14:54:50,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,778] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,778] [INFO] Running command: gunzip -c /var/lib/cwl/stge46dee8d-c0d4-48b7-9b79-f6cbb2d3882d/GCF_004000435.1_ASM400043v1_genomic.fna.gz | prodigal -d GCF_004000435.1_ASM400043v1_genomic.fna/cds.fna -a GCF_004000435.1_ASM400043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:04,287] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:04,287] [INFO] Task started: HMMsearch
[2024-01-24 14:55:04,288] [INFO] Running command: hmmsearch --tblout GCF_004000435.1_ASM400043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference/reference_markers.hmm GCF_004000435.1_ASM400043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:04,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:04,560] [INFO] Found 6/6 markers.
[2024-01-24 14:55:04,609] [INFO] Query marker FASTA was written to GCF_004000435.1_ASM400043v1_genomic.fna/markers.fasta
[2024-01-24 14:55:04,610] [INFO] Task started: Blastn
[2024-01-24 14:55:04,610] [INFO] Running command: blastn -query GCF_004000435.1_ASM400043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference/reference_markers.fasta -out GCF_004000435.1_ASM400043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:05,564] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:05,566] [INFO] Selected 26 target genomes.
[2024-01-24 14:55:05,567] [INFO] Target genome list was writen to GCF_004000435.1_ASM400043v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:05,895] [INFO] Task started: fastANI
[2024-01-24 14:55:05,896] [INFO] Running command: fastANI --query /var/lib/cwl/stge46dee8d-c0d4-48b7-9b79-f6cbb2d3882d/GCF_004000435.1_ASM400043v1_genomic.fna.gz --refList GCF_004000435.1_ASM400043v1_genomic.fna/target_genomes.txt --output GCF_004000435.1_ASM400043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:24,496] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:24,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:24,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:24,521] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:24,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:24,522] [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
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	100.0	1498	1503	95	conclusive
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.872	264	1503	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.6167	393	1503	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.4789	391	1503	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.385	401	1503	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.3626	394	1503	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.2815	426	1503	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.2678	400	1503	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.2394	368	1503	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.1664	412	1503	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.1061	347	1503	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.0684	437	1503	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.0668	380	1503	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.0362	399	1503	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.9888	413	1503	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.9787	411	1503	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9675	379	1503	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.9552	422	1503	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.95	353	1503	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.9053	357	1503	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	77.8972	431	1503	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.7742	339	1503	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.7678	353	1503	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6989	380	1503	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.6322	346	1503	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.3431	234	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:24,523] [INFO] DFAST Taxonomy check result was written to GCF_004000435.1_ASM400043v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:24,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:24,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:24,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference/checkm_data
[2024-01-24 14:55:24,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:24,569] [INFO] Task started: CheckM
[2024-01-24 14:55:24,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004000435.1_ASM400043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004000435.1_ASM400043v1_genomic.fna/checkm_input GCF_004000435.1_ASM400043v1_genomic.fna/checkm_result
[2024-01-24 14:56:11,530] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:11,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:11,548] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:11,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:11,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004000435.1_ASM400043v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:11,549] [INFO] Task started: Blastn
[2024-01-24 14:56:11,549] [INFO] Running command: blastn -query GCF_004000435.1_ASM400043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e1d3b88-c586-4db1-8258-966caf721a56/dqc_reference/reference_markers_gtdb.fasta -out GCF_004000435.1_ASM400043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:13,313] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:13,317] [INFO] Selected 26 target genomes.
[2024-01-24 14:56:13,317] [INFO] Target genome list was writen to GCF_004000435.1_ASM400043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:13,336] [INFO] Task started: fastANI
[2024-01-24 14:56:13,337] [INFO] Running command: fastANI --query /var/lib/cwl/stge46dee8d-c0d4-48b7-9b79-f6cbb2d3882d/GCF_004000435.1_ASM400043v1_genomic.fna.gz --refList GCF_004000435.1_ASM400043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004000435.1_ASM400043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:32,716] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:32,738] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:32,738] [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_004000435.1	s__Flavimaricola sp004000435	100.0	1498	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	conclusive
GCF_002814095.1	s__Sagittula sp002814095	79.0098	408	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.6165	393	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900184895.1	s__Flavimaricola marinus	78.5334	505	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172355.1	s__Oceanicola antarcticus	78.4076	498	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.3736	277	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.2957	396	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.2756	426	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993005.1	s__JAACUH01 sp009993005	78.1914	475	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.1513	413	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.1356	380	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.0923	349	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.0769	436	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	78.0593	411	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	78.0539	253	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.0511	396	1503	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_014637725.1	s__Marivita lacus	77.9973	412	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	77.9824	382	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	77.9705	412	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_004145405.1	s__Loktanella sp004145405	77.9553	361	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	77.8513	327	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_013032855.1	s__Ruegeria arenilitoris	77.8487	313	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	77.7634	352	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.7499	356	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	77.6885	354	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	77.3435	234	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:32,740] [INFO] GTDB search result was written to GCF_004000435.1_ASM400043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:32,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:32,746] [INFO] DFAST_QC result json was written to GCF_004000435.1_ASM400043v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:32,747] [INFO] DFAST_QC completed!
[2024-01-24 14:56:32,747] [INFO] Total running time: 0h1m43s