[2024-01-24 12:06:14,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference
[2024-01-24 12:06:16,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,190] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d116702-644a-44a3-81a8-d7e4fa7c53e9/GCF_014201905.1_ASM1420190v1_genomic.fna.gz | prodigal -d GCF_014201905.1_ASM1420190v1_genomic.fna/cds.fna -a GCF_014201905.1_ASM1420190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:29,980] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:29,980] [INFO] Task started: HMMsearch
[2024-01-24 12:06:29,980] [INFO] Running command: hmmsearch --tblout GCF_014201905.1_ASM1420190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference/reference_markers.hmm GCF_014201905.1_ASM1420190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,305] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,346] [INFO] Query marker FASTA was written to GCF_014201905.1_ASM1420190v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,346] [INFO] Task started: Blastn
[2024-01-24 12:06:30,346] [INFO] Running command: blastn -query GCF_014201905.1_ASM1420190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference/reference_markers.fasta -out GCF_014201905.1_ASM1420190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:31,427] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:31,431] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:31,431] [INFO] Target genome list was writen to GCF_014201905.1_ASM1420190v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:31,437] [INFO] Task started: fastANI
[2024-01-24 12:06:31,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d116702-644a-44a3-81a8-d7e4fa7c53e9/GCF_014201905.1_ASM1420190v1_genomic.fna.gz --refList GCF_014201905.1_ASM1420190v1_genomic.fna/target_genomes.txt --output GCF_014201905.1_ASM1420190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:45,905] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:45,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:45,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:45,920] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:45,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:45,921] [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
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	100.0	1599	1600	95	conclusive
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	79.7333	678	1600	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.322	451	1600	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	77.871	423	1600	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.8338	313	1600	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.7452	328	1600	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	77.6483	400	1600	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	77.6425	400	1600	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	77.5671	399	1600	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	77.56	410	1600	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	77.5213	303	1600	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.3876	349	1600	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.3698	349	1600	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.3608	308	1600	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	77.2868	333	1600	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	77.2835	248	1600	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.1353	280	1600	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	76.9408	211	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:45,923] [INFO] DFAST Taxonomy check result was written to GCF_014201905.1_ASM1420190v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:45,923] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:45,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:45,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference/checkm_data
[2024-01-24 12:06:45,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:45,976] [INFO] Task started: CheckM
[2024-01-24 12:06:45,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201905.1_ASM1420190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201905.1_ASM1420190v1_genomic.fna/checkm_input GCF_014201905.1_ASM1420190v1_genomic.fna/checkm_result
[2024-01-24 12:07:36,650] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:36,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,675] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:36,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:36,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201905.1_ASM1420190v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:36,676] [INFO] Task started: Blastn
[2024-01-24 12:07:36,676] [INFO] Running command: blastn -query GCF_014201905.1_ASM1420190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6f1c0d-355f-4084-a449-b91697cf61ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201905.1_ASM1420190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:38,618] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:38,622] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:38,622] [INFO] Target genome list was writen to GCF_014201905.1_ASM1420190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:38,647] [INFO] Task started: fastANI
[2024-01-24 12:07:38,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d116702-644a-44a3-81a8-d7e4fa7c53e9/GCF_014201905.1_ASM1420190v1_genomic.fna.gz --refList GCF_014201905.1_ASM1420190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201905.1_ASM1420190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:48,222] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:48,236] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:48,236] [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_014201905.1	s__Amaricoccus macauensis	100.0	1599	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017993425.1	s__Amaricoccus sp017993425	79.759	673	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	79.7339	677	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	79.6574	667	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	79.4879	535	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	79.1236	485	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119835.1	s__SKOX01 sp007119835	78.7487	332	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SKOX01	95.0	99.00	98.89	0.80	0.77	3	-
GCF_003385555.1	s__Rhodosalinus sediminis	77.9741	356	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004146235.1	s__Tropicimonas sp004146235	77.1421	302	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	76.9522	210	1600	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_016888515.1	s__Shimia_A biformata	76.6659	147	1600	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:48,238] [INFO] GTDB search result was written to GCF_014201905.1_ASM1420190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:48,239] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:48,242] [INFO] DFAST_QC result json was written to GCF_014201905.1_ASM1420190v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:48,243] [INFO] DFAST_QC completed!
[2024-01-24 12:07:48,243] [INFO] Total running time: 0h1m33s