[2024-01-24 13:25:31,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference
[2024-01-24 13:25:32,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,574] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,574] [INFO] Running command: gunzip -c /var/lib/cwl/stge68655cc-b19e-4128-9a6f-3f606b7c1611/GCF_004339595.1_ASM433959v1_genomic.fna.gz | prodigal -d GCF_004339595.1_ASM433959v1_genomic.fna/cds.fna -a GCF_004339595.1_ASM433959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:45,981] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:45,981] [INFO] Task started: HMMsearch
[2024-01-24 13:25:45,981] [INFO] Running command: hmmsearch --tblout GCF_004339595.1_ASM433959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference/reference_markers.hmm GCF_004339595.1_ASM433959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:46,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:46,288] [INFO] Found 6/6 markers.
[2024-01-24 13:25:46,347] [INFO] Query marker FASTA was written to GCF_004339595.1_ASM433959v1_genomic.fna/markers.fasta
[2024-01-24 13:25:46,347] [INFO] Task started: Blastn
[2024-01-24 13:25:46,347] [INFO] Running command: blastn -query GCF_004339595.1_ASM433959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference/reference_markers.fasta -out GCF_004339595.1_ASM433959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:47,121] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:47,124] [INFO] Selected 21 target genomes.
[2024-01-24 13:25:47,125] [INFO] Target genome list was writen to GCF_004339595.1_ASM433959v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:47,133] [INFO] Task started: fastANI
[2024-01-24 13:25:47,134] [INFO] Running command: fastANI --query /var/lib/cwl/stge68655cc-b19e-4128-9a6f-3f606b7c1611/GCF_004339595.1_ASM433959v1_genomic.fna.gz --refList GCF_004339595.1_ASM433959v1_genomic.fna/target_genomes.txt --output GCF_004339595.1_ASM433959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:07,298] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:07,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:07,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:07,319] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:07,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:07,320] [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
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	100.0	1652	1653	95	conclusive
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	90.7161	1431	1653	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	80.0733	626	1653	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	79.9214	638	1653	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	79.7013	517	1653	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	78.972	296	1653	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	78.9609	364	1653	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	78.8612	279	1653	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	78.4156	335	1653	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.8217	262	1653	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.7652	245	1653	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.7585	271	1653	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5933	151	1653	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.561	172	1653	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	76.5368	108	1653	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.4941	146	1653	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.4585	150	1653	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	76.3785	164	1653	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.3783	149	1653	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	76.1154	143	1653	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	75.2606	51	1653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:07,321] [INFO] DFAST Taxonomy check result was written to GCF_004339595.1_ASM433959v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:07,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:07,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:07,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference/checkm_data
[2024-01-24 13:26:07,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:07,373] [INFO] Task started: CheckM
[2024-01-24 13:26:07,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339595.1_ASM433959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339595.1_ASM433959v1_genomic.fna/checkm_input GCF_004339595.1_ASM433959v1_genomic.fna/checkm_result
[2024-01-24 13:26:49,045] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:49,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:49,071] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:49,071] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:49,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339595.1_ASM433959v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:49,072] [INFO] Task started: Blastn
[2024-01-24 13:26:49,072] [INFO] Running command: blastn -query GCF_004339595.1_ASM433959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153473ed-3bfd-4d28-b51f-bf21d8b5f576/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339595.1_ASM433959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:50,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:50,087] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:50,087] [INFO] Target genome list was writen to GCF_004339595.1_ASM433959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:50,098] [INFO] Task started: fastANI
[2024-01-24 13:26:50,098] [INFO] Running command: fastANI --query /var/lib/cwl/stge68655cc-b19e-4128-9a6f-3f606b7c1611/GCF_004339595.1_ASM433959v1_genomic.fna.gz --refList GCF_004339595.1_ASM433959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339595.1_ASM433959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:58,707] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:58,720] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:58,720] [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_004339595.1	s__Marinobacterium mangrovicola	100.0	1652	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900108065.1	s__Marinobacterium lutimaris	90.6964	1433	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	80.0692	624	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250495.1	s__Marinobacterium sp003250495	79.9229	404	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	79.9175	638	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000705555.1	s__Marinobacterium sp000705555	79.7452	521	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCF_000428985.1	s__Marinobacterium litorale	79.686	519	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCF_019061305.1	s__Marinobacterium sp019061305	78.8347	314	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868415.1	s__Marinobacterium sp013868415	78.4482	273	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	77.0615	128	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:58,722] [INFO] GTDB search result was written to GCF_004339595.1_ASM433959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:58,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:58,726] [INFO] DFAST_QC result json was written to GCF_004339595.1_ASM433959v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:58,726] [INFO] DFAST_QC completed!
[2024-01-24 13:26:58,726] [INFO] Total running time: 0h1m27s