[2024-01-24 13:57:40,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:40,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:40,384] [INFO] DQC Reference Directory: /var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference
[2024-01-24 13:57:41,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:41,583] [INFO] Task started: Prodigal
[2024-01-24 13:57:41,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg4943b493-3ac5-4c75-98b8-c8fe4fec8ebd/GCF_016019955.1_ASM1601995v1_genomic.fna.gz | prodigal -d GCF_016019955.1_ASM1601995v1_genomic.fna/cds.fna -a GCF_016019955.1_ASM1601995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,015] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,016] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,016] [INFO] Running command: hmmsearch --tblout GCF_016019955.1_ASM1601995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference/reference_markers.hmm GCF_016019955.1_ASM1601995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:55,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:55,255] [INFO] Found 6/6 markers.
[2024-01-24 13:57:55,295] [INFO] Query marker FASTA was written to GCF_016019955.1_ASM1601995v1_genomic.fna/markers.fasta
[2024-01-24 13:57:55,296] [INFO] Task started: Blastn
[2024-01-24 13:57:55,296] [INFO] Running command: blastn -query GCF_016019955.1_ASM1601995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference/reference_markers.fasta -out GCF_016019955.1_ASM1601995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,057] [INFO] Selected 30 target genomes.
[2024-01-24 13:57:56,057] [INFO] Target genome list was writen to GCF_016019955.1_ASM1601995v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:56,070] [INFO] Task started: fastANI
[2024-01-24 13:57:56,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg4943b493-3ac5-4c75-98b8-c8fe4fec8ebd/GCF_016019955.1_ASM1601995v1_genomic.fna.gz --refList GCF_016019955.1_ASM1601995v1_genomic.fna/target_genomes.txt --output GCF_016019955.1_ASM1601995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:19,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:19,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:19,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:19,568] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:19,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:19,569] [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 atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	79.5435	453	1357	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.9734	532	1357	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.9623	519	1357	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.8998	508	1357	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.8702	510	1357	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.858	452	1357	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.8001	457	1357	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	78.7451	546	1357	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.7252	518	1357	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.689	491	1357	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.6554	474	1357	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.6512	529	1357	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.4571	450	1357	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	78.4065	525	1357	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.3405	456	1357	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.3175	451	1357	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.2798	461	1357	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	78.1377	445	1357	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.0287	434	1357	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.9417	383	1357	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.9096	372	1357	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.8047	377	1357	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.7954	405	1357	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6864	321	1357	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.561	330	1357	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.553	329	1357	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	77.491	310	1357	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.4366	365	1357	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4246	346	1357	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.9752	204	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:19,571] [INFO] DFAST Taxonomy check result was written to GCF_016019955.1_ASM1601995v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:19,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:19,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:19,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference/checkm_data
[2024-01-24 13:58:19,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:19,623] [INFO] Task started: CheckM
[2024-01-24 13:58:19,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016019955.1_ASM1601995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016019955.1_ASM1601995v1_genomic.fna/checkm_input GCF_016019955.1_ASM1601995v1_genomic.fna/checkm_result
[2024-01-24 13:59:05,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:05,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,332] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:05,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:05,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016019955.1_ASM1601995v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:05,333] [INFO] Task started: Blastn
[2024-01-24 13:59:05,333] [INFO] Running command: blastn -query GCF_016019955.1_ASM1601995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf093d3-3228-4fcb-8982-3f500dbc5df9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016019955.1_ASM1601995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:06,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:06,670] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:06,670] [INFO] Target genome list was writen to GCF_016019955.1_ASM1601995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:06,686] [INFO] Task started: fastANI
[2024-01-24 13:59:06,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg4943b493-3ac5-4c75-98b8-c8fe4fec8ebd/GCF_016019955.1_ASM1601995v1_genomic.fna.gz --refList GCF_016019955.1_ASM1601995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016019955.1_ASM1601995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:22,962] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:22,977] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:22,978] [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_016019955.1	s__Shimia sp016019955	100.0	1354	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	conclusive
GCF_900114635.1	s__Shimia aestuarii	81.3366	835	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	80.3725	628	1357	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_900142185.1	s__Lutimaribacter pacificus	80.2603	569	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900182725.1	s__Thalassobius litoralis	79.5073	401	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	78.9731	519	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.9149	505	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.8617	511	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	78.8159	455	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_003990645.1	s__Shimia sediminis	78.7414	546	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.6435	530	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.6183	496	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013031405.1	s__Ruegeria sp013031405	78.527	492	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014475.1	s__Shimia abyssi	78.3991	526	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.3152	459	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	78.2797	461	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	78.1701	455	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_900114415.1	s__Shimia haliotis	78.1472	442	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	77.7176	387	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCA_002709405.1	s__Marinibacterium sp002709405	77.4622	426	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,979] [INFO] GTDB search result was written to GCF_016019955.1_ASM1601995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:22,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:22,986] [INFO] DFAST_QC result json was written to GCF_016019955.1_ASM1601995v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:22,986] [INFO] DFAST_QC completed!
[2024-01-24 13:59:22,986] [INFO] Total running time: 0h1m43s