[2024-01-24 12:06:24,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference
[2024-01-24 12:06:25,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,935] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg129c3336-1d47-4228-8032-47f603f72d46/GCF_003260265.1_ASM326026v1_genomic.fna.gz | prodigal -d GCF_003260265.1_ASM326026v1_genomic.fna/cds.fna -a GCF_003260265.1_ASM326026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:37,225] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:37,225] [INFO] Task started: HMMsearch
[2024-01-24 12:06:37,225] [INFO] Running command: hmmsearch --tblout GCF_003260265.1_ASM326026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference/reference_markers.hmm GCF_003260265.1_ASM326026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:37,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:37,469] [INFO] Found 6/6 markers.
[2024-01-24 12:06:37,505] [INFO] Query marker FASTA was written to GCF_003260265.1_ASM326026v1_genomic.fna/markers.fasta
[2024-01-24 12:06:37,505] [INFO] Task started: Blastn
[2024-01-24 12:06:37,505] [INFO] Running command: blastn -query GCF_003260265.1_ASM326026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference/reference_markers.fasta -out GCF_003260265.1_ASM326026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,407] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,410] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:38,410] [INFO] Target genome list was writen to GCF_003260265.1_ASM326026v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:38,416] [INFO] Task started: fastANI
[2024-01-24 12:06:38,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg129c3336-1d47-4228-8032-47f603f72d46/GCF_003260265.1_ASM326026v1_genomic.fna.gz --refList GCF_003260265.1_ASM326026v1_genomic.fna/target_genomes.txt --output GCF_003260265.1_ASM326026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:52,195] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:52,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:52,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:52,210] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:52,210] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:52,210] [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
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	80.3846	709	1232	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	80.3551	721	1232	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	80.2694	704	1232	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	80.0711	607	1232	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	80.0203	614	1232	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	80.0111	609	1232	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	79.7808	623	1232	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.487	582	1232	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.34	540	1232	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.1661	528	1232	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.8032	477	1232	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5982	442	1232	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.5241	463	1232	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	78.4674	456	1232	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.2199	353	1232	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.163	387	1232	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.6043	344	1232	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.231	350	1232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:52,212] [INFO] DFAST Taxonomy check result was written to GCF_003260265.1_ASM326026v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:52,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:52,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:52,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference/checkm_data
[2024-01-24 12:06:52,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:52,251] [INFO] Task started: CheckM
[2024-01-24 12:06:52,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003260265.1_ASM326026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003260265.1_ASM326026v1_genomic.fna/checkm_input GCF_003260265.1_ASM326026v1_genomic.fna/checkm_result
[2024-01-24 12:07:28,055] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:28,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:28,074] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:28,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:28,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003260265.1_ASM326026v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:28,075] [INFO] Task started: Blastn
[2024-01-24 12:07:28,075] [INFO] Running command: blastn -query GCF_003260265.1_ASM326026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc95847f-523d-41fc-a2ba-fdc4384e849c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003260265.1_ASM326026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:29,556] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:29,559] [INFO] Selected 22 target genomes.
[2024-01-24 12:07:29,559] [INFO] Target genome list was writen to GCF_003260265.1_ASM326026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:29,574] [INFO] Task started: fastANI
[2024-01-24 12:07:29,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg129c3336-1d47-4228-8032-47f603f72d46/GCF_003260265.1_ASM326026v1_genomic.fna.gz --refList GCF_003260265.1_ASM326026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003260265.1_ASM326026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:46,751] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:46,768] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:46,768] [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_003260265.1	s__Roseovarius sp003260265	100.0	1231	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008728195.1	s__Roseovarius indicus	80.3822	710	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900142665.1	s__Roseovarius pacificus	80.0846	606	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900172255.1	s__Roseovarius halotolerans	80.0023	617	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001441615.1	s__Roseovarius atlanticus	79.7678	625	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	79.598	583	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.479	583	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	79.3438	572	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	79.3334	559	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	79.3136	543	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCA_002166865.1	s__Roseovarius sp002166865	79.1988	524	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	79.1703	527	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCA_002842985.1	s__Roseovarius sp002842985	79.0921	515	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	79.0808	523	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	78.962	493	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	78.9612	531	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.7944	478	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761875.1	s__Roseovarius aestuariivivens	78.4849	455	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.4282	404	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	78.2111	475	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	77.9177	412	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423085.1	s__Methylobacterium sp001423085	75.7765	91	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.83	97.83	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:46,770] [INFO] GTDB search result was written to GCF_003260265.1_ASM326026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:46,770] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:46,774] [INFO] DFAST_QC result json was written to GCF_003260265.1_ASM326026v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:46,774] [INFO] DFAST_QC completed!
[2024-01-24 12:07:46,774] [INFO] Total running time: 0h1m22s