[2024-01-24 14:20:14,409] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference
[2024-01-24 14:20:15,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,787] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg61a9292e-ad16-4b4a-8614-1357d9f03070/GCF_019966515.1_ASM1996651v1_genomic.fna.gz | prodigal -d GCF_019966515.1_ASM1996651v1_genomic.fna/cds.fna -a GCF_019966515.1_ASM1996651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:30,365] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:30,366] [INFO] Task started: HMMsearch
[2024-01-24 14:20:30,366] [INFO] Running command: hmmsearch --tblout GCF_019966515.1_ASM1996651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference/reference_markers.hmm GCF_019966515.1_ASM1996651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:30,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:30,642] [INFO] Found 6/6 markers.
[2024-01-24 14:20:30,698] [INFO] Query marker FASTA was written to GCF_019966515.1_ASM1996651v1_genomic.fna/markers.fasta
[2024-01-24 14:20:30,698] [INFO] Task started: Blastn
[2024-01-24 14:20:30,699] [INFO] Running command: blastn -query GCF_019966515.1_ASM1996651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference/reference_markers.fasta -out GCF_019966515.1_ASM1996651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:31,607] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:31,610] [INFO] Selected 24 target genomes.
[2024-01-24 14:20:31,611] [INFO] Target genome list was writen to GCF_019966515.1_ASM1996651v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:31,643] [INFO] Task started: fastANI
[2024-01-24 14:20:31,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg61a9292e-ad16-4b4a-8614-1357d9f03070/GCF_019966515.1_ASM1996651v1_genomic.fna.gz --refList GCF_019966515.1_ASM1996651v1_genomic.fna/target_genomes.txt --output GCF_019966515.1_ASM1996651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:50,086] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:50,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:50,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:50,104] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:50,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:50,105] [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 aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	100.0	1548	1551	95	conclusive
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.5861	457	1551	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.5666	497	1551	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.527	461	1551	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.4039	440	1551	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.3632	417	1551	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.3539	416	1551	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.3531	413	1551	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.2488	410	1551	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.0766	392	1551	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.9514	442	1551	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.8983	337	1551	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.7885	351	1551	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.7498	316	1551	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.6444	275	1551	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.6363	282	1551	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.6024	345	1551	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.5824	285	1551	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.5411	337	1551	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4757	255	1551	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0919	213	1551	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.7553	230	1551	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.6474	144	1551	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.4908	145	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:50,111] [INFO] DFAST Taxonomy check result was written to GCF_019966515.1_ASM1996651v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:50,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:50,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:50,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference/checkm_data
[2024-01-24 14:20:50,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:50,161] [INFO] Task started: CheckM
[2024-01-24 14:20:50,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019966515.1_ASM1996651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019966515.1_ASM1996651v1_genomic.fna/checkm_input GCF_019966515.1_ASM1996651v1_genomic.fna/checkm_result
[2024-01-24 14:21:32,153] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:32,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:32,173] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:32,173] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:32,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019966515.1_ASM1996651v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:32,173] [INFO] Task started: Blastn
[2024-01-24 14:21:32,174] [INFO] Running command: blastn -query GCF_019966515.1_ASM1996651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd55d22d-58ae-4ab0-aede-ba25bad777ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_019966515.1_ASM1996651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:33,554] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:33,558] [INFO] Selected 22 target genomes.
[2024-01-24 14:21:33,558] [INFO] Target genome list was writen to GCF_019966515.1_ASM1996651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:33,634] [INFO] Task started: fastANI
[2024-01-24 14:21:33,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg61a9292e-ad16-4b4a-8614-1357d9f03070/GCF_019966515.1_ASM1996651v1_genomic.fna.gz --refList GCF_019966515.1_ASM1996651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019966515.1_ASM1996651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:49,493] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:49,509] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:49,510] [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_900172285.1	s__Roseovarius aestuarii	99.9993	1550	1551	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_900142665.1	s__Roseovarius pacificus	78.5727	458	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_009762325.1	s__Roseovarius faecimaris	78.5668	497	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	78.4039	440	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_008728195.1	s__Roseovarius indicus	78.3619	412	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900142765.1	s__Roseovarius litoreus	78.2394	411	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_900109855.1	s__Roseovarius tolerans	78.1431	419	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.1025	400	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003072125.1	s__Roseovarius sediminicola	78.0861	391	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.0789	297	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_900129345.1	s__Ruegeria intermedia	78.0668	342	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.9279	334	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	77.8072	333	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.7974	350	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	77.7498	316	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990645.1	s__Shimia sediminis	77.6562	274	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	77.6222	346	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.6117	344	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	77.5937	284	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.4819	321	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.4	247	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	77.1019	276	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:49,511] [INFO] GTDB search result was written to GCF_019966515.1_ASM1996651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:49,512] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:49,516] [INFO] DFAST_QC result json was written to GCF_019966515.1_ASM1996651v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:49,516] [INFO] DFAST_QC completed!
[2024-01-24 14:21:49,516] [INFO] Total running time: 0h1m35s