[2024-01-24 13:57:42,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference
[2024-01-24 13:57:44,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,177] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea868a4-7d09-4e47-9744-8afdd9f0efae/GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/cds.fna -a GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:59,234] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:59,235] [INFO] Task started: HMMsearch
[2024-01-24 13:57:59,235] [INFO] Running command: hmmsearch --tblout GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference/reference_markers.hmm GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:59,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:59,624] [INFO] Found 6/6 markers.
[2024-01-24 13:57:59,678] [INFO] Query marker FASTA was written to GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:59,679] [INFO] Task started: Blastn
[2024-01-24 13:57:59,679] [INFO] Running command: blastn -query GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference/reference_markers.fasta -out GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,763] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:00,763] [INFO] Target genome list was writen to GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,769] [INFO] Task started: fastANI
[2024-01-24 13:58:00,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea868a4-7d09-4e47-9744-8afdd9f0efae/GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna.gz --refList GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:24,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:24,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:24,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:25,005] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:25,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:25,005] [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
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	100.0	1971	1973	95	conclusive
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	81.8272	1132	1973	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.9589	692	1973	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	78.2957	707	1973	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.2145	649	1973	95	below_threshold
Thermohalobaculum xanthum	strain=M0105	GCA_016623495.1	2753746	2753746	type	True	78.0765	507	1973	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.0248	615	1973	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.8216	632	1973	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.78	512	1973	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	77.1992	498	1973	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	77.1769	508	1973	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.1154	506	1973	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	77.1082	510	1973	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	77.0852	439	1973	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.0649	572	1973	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.4411	271	1973	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.3536	261	1973	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.1941	202	1973	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.1083	675	1973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,007] [INFO] DFAST Taxonomy check result was written to GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:25,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:25,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:25,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference/checkm_data
[2024-01-24 13:58:25,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:25,087] [INFO] Task started: CheckM
[2024-01-24 13:58:25,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/checkm_input GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:37,366] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:37,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:37,388] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:37,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:37,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:37,389] [INFO] Task started: Blastn
[2024-01-24 13:59:37,389] [INFO] Running command: blastn -query GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f8d9d2c-d34f-4ab6-a971-15783923d425/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:38,975] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:38,979] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:38,979] [INFO] Target genome list was writen to GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:39,006] [INFO] Task started: fastANI
[2024-01-24 13:59:39,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea868a4-7d09-4e47-9744-8afdd9f0efae/GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna.gz --refList GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:56,479] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:56,495] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:56,495] [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_900113695.1	s__Albimonas pacifica	100.0	1971	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106695.1	s__Albimonas donghaensis	81.7986	1137	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_008124525.1	s__Oceanicella actignis	78.8894	703	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_003448965.1	s__Paroceanicella sp003448965	78.5501	799	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	78.2841	708	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623495.1	s__Limibaculum sp016623495	78.055	510	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.0232	615	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	77.6297	587	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	77.5956	587	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	77.4592	580	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	77.3705	629	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.3203	740	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	77.1039	428	1973	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:56,497] [INFO] GTDB search result was written to GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:56,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:56,504] [INFO] DFAST_QC result json was written to GCF_900113695.1_IMG-taxon_2667527406_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:56,505] [INFO] DFAST_QC completed!
[2024-01-24 13:59:56,505] [INFO] Total running time: 0h2m14s