[2024-01-25 18:41:35,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:35,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:35,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference
[2024-01-25 18:41:36,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:36,664] [INFO] Task started: Prodigal
[2024-01-25 18:41:36,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg7029a7bc-e087-4cdd-b591-d20d555acead/GCF_003072125.1_ASM307212v1_genomic.fna.gz | prodigal -d GCF_003072125.1_ASM307212v1_genomic.fna/cds.fna -a GCF_003072125.1_ASM307212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:47,251] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:47,251] [INFO] Task started: HMMsearch
[2024-01-25 18:41:47,251] [INFO] Running command: hmmsearch --tblout GCF_003072125.1_ASM307212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference/reference_markers.hmm GCF_003072125.1_ASM307212v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:47,465] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:47,467] [INFO] Found 6/6 markers.
[2024-01-25 18:41:47,500] [INFO] Query marker FASTA was written to GCF_003072125.1_ASM307212v1_genomic.fna/markers.fasta
[2024-01-25 18:41:47,500] [INFO] Task started: Blastn
[2024-01-25 18:41:47,500] [INFO] Running command: blastn -query GCF_003072125.1_ASM307212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference/reference_markers.fasta -out GCF_003072125.1_ASM307212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:48,486] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:48,489] [INFO] Selected 23 target genomes.
[2024-01-25 18:41:48,489] [INFO] Target genome list was writen to GCF_003072125.1_ASM307212v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:48,503] [INFO] Task started: fastANI
[2024-01-25 18:41:48,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg7029a7bc-e087-4cdd-b591-d20d555acead/GCF_003072125.1_ASM307212v1_genomic.fna.gz --refList GCF_003072125.1_ASM307212v1_genomic.fna/target_genomes.txt --output GCF_003072125.1_ASM307212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:06,263] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:06,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:06,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:06,278] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:06,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:06,279] [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
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	100.0	1286	1291	95	conclusive
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	84.8252	835	1291	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.6252	519	1291	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.5842	522	1291	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.3903	497	1291	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	79.2472	516	1291	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	79.1479	516	1291	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	79.0096	483	1291	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	78.9775	480	1291	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.9144	516	1291	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.547	419	1291	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.5425	413	1291	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.4441	494	1291	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.4103	435	1291	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.3918	443	1291	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.3596	438	1291	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.1935	379	1291	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.1408	399	1291	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.1146	404	1291	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	78.0547	353	1291	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9082	331	1291	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8944	364	1291	95	below_threshold
Pontibaca salina	strain=S1109L	GCA_016307205.1	2795731	2795731	type	True	77.2619	277	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:06,281] [INFO] DFAST Taxonomy check result was written to GCF_003072125.1_ASM307212v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:06,281] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:06,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:06,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference/checkm_data
[2024-01-25 18:42:06,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:06,326] [INFO] Task started: CheckM
[2024-01-25 18:42:06,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003072125.1_ASM307212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003072125.1_ASM307212v1_genomic.fna/checkm_input GCF_003072125.1_ASM307212v1_genomic.fna/checkm_result
[2024-01-25 18:42:41,522] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:41,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:41,547] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:41,548] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:41,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003072125.1_ASM307212v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:41,548] [INFO] Task started: Blastn
[2024-01-25 18:42:41,548] [INFO] Running command: blastn -query GCF_003072125.1_ASM307212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg088c31cb-a8b8-4e45-8f80-9928b2034fc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003072125.1_ASM307212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:43,531] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:43,535] [INFO] Selected 11 target genomes.
[2024-01-25 18:42:43,535] [INFO] Target genome list was writen to GCF_003072125.1_ASM307212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:43,606] [INFO] Task started: fastANI
[2024-01-25 18:42:43,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg7029a7bc-e087-4cdd-b591-d20d555acead/GCF_003072125.1_ASM307212v1_genomic.fna.gz --refList GCF_003072125.1_ASM307212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003072125.1_ASM307212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:53,579] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:53,587] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:53,587] [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_003072125.1	s__Roseovarius sediminicola	100.0	1286	1291	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_003316635.1	s__Roseovarius dicentrarchi	84.8031	837	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	82.7387	775	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003651245.1	s__Roseovarius spongiae	80.7624	653	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006125015.1	s__Roseovarius arcticus	80.6701	676	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260265.1	s__Roseovarius sp003260265	79.0352	518	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002925845.1	s__Roseovarius nitratireducens	78.9841	484	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_002917925.1	s__Roseovarius confluentis	78.9058	517	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_003344785.1	s__Puniceibacterium profundi	78.7192	464	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	78.2882	429	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	78.1423	399	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:53,589] [INFO] GTDB search result was written to GCF_003072125.1_ASM307212v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:53,589] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:53,596] [INFO] DFAST_QC result json was written to GCF_003072125.1_ASM307212v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:53,596] [INFO] DFAST_QC completed!
[2024-01-25 18:42:53,596] [INFO] Total running time: 0h1m18s