[2024-01-24 14:54:56,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference
[2024-01-24 14:54:58,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,197] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,198] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fa10642-d76b-4f7f-9b97-1b01a21e7d1b/GCF_007923355.1_ASM792335v1_genomic.fna.gz | prodigal -d GCF_007923355.1_ASM792335v1_genomic.fna/cds.fna -a GCF_007923355.1_ASM792335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:13,979] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:13,980] [INFO] Task started: HMMsearch
[2024-01-24 14:55:13,980] [INFO] Running command: hmmsearch --tblout GCF_007923355.1_ASM792335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference/reference_markers.hmm GCF_007923355.1_ASM792335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:14,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:14,285] [INFO] Found 6/6 markers.
[2024-01-24 14:55:14,333] [INFO] Query marker FASTA was written to GCF_007923355.1_ASM792335v1_genomic.fna/markers.fasta
[2024-01-24 14:55:14,334] [INFO] Task started: Blastn
[2024-01-24 14:55:14,334] [INFO] Running command: blastn -query GCF_007923355.1_ASM792335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference/reference_markers.fasta -out GCF_007923355.1_ASM792335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:15,133] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:15,137] [INFO] Selected 25 target genomes.
[2024-01-24 14:55:15,137] [INFO] Target genome list was writen to GCF_007923355.1_ASM792335v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:15,150] [INFO] Task started: fastANI
[2024-01-24 14:55:15,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fa10642-d76b-4f7f-9b97-1b01a21e7d1b/GCF_007923355.1_ASM792335v1_genomic.fna.gz --refList GCF_007923355.1_ASM792335v1_genomic.fna/target_genomes.txt --output GCF_007923355.1_ASM792335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:36,012] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:36,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:36,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:36,032] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:36,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:36,032] [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
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	100.0	1618	1618	95	conclusive
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.238	467	1618	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.1269	477	1618	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.1138	526	1618	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.1055	498	1618	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	78.0047	487	1618	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.958	415	1618	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	77.9409	386	1618	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	77.8068	395	1618	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.8042	406	1618	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	77.7609	386	1618	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	77.7479	324	1618	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.6888	453	1618	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.688	457	1618	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.6484	345	1618	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	77.5671	326	1618	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	77.4784	356	1618	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	77.2319	337	1618	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.1544	265	1618	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.1114	325	1618	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.9647	283	1618	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.8437	221	1618	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.7753	149	1618	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.4388	185	1618	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.2512	156	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:36,042] [INFO] DFAST Taxonomy check result was written to GCF_007923355.1_ASM792335v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:36,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:36,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:36,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference/checkm_data
[2024-01-24 14:55:36,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:36,096] [INFO] Task started: CheckM
[2024-01-24 14:55:36,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007923355.1_ASM792335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007923355.1_ASM792335v1_genomic.fna/checkm_input GCF_007923355.1_ASM792335v1_genomic.fna/checkm_result
[2024-01-24 14:56:25,096] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:25,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:25,117] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:25,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:25,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007923355.1_ASM792335v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:25,119] [INFO] Task started: Blastn
[2024-01-24 14:56:25,119] [INFO] Running command: blastn -query GCF_007923355.1_ASM792335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4530cd29-5ff6-4204-a264-9a27c9044a8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007923355.1_ASM792335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:26,424] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:26,428] [INFO] Selected 28 target genomes.
[2024-01-24 14:56:26,428] [INFO] Target genome list was writen to GCF_007923355.1_ASM792335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:26,448] [INFO] Task started: fastANI
[2024-01-24 14:56:26,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fa10642-d76b-4f7f-9b97-1b01a21e7d1b/GCF_007923355.1_ASM792335v1_genomic.fna.gz --refList GCF_007923355.1_ASM792335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007923355.1_ASM792335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:48,862] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:48,883] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:48,883] [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_007923355.1	s__Phaeobacter_A marinintestinus	100.0	1618	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.2445	475	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.1273	524	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	78.1234	430	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.1053	433	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	78.0475	447	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	78.0474	444	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_900302455.1	s__Ruegeria_E mediterranea	78.0055	487	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	77.9343	432	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872875.1	s__WKFI01 sp014872875	77.9278	422	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	77.9061	413	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033965.1	s__Ruegeria atlantica_D	77.9028	367	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	77.8999	459	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000203975.2	s__Leisingera sp000203975	77.8807	386	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.8434	395	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	77.8293	444	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123675.1	s__Leisingera sp004123675	77.7722	408	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_001679925.1	s__Leisingera sp001679925	77.7441	377	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182615.1	s__Ruegeria faecimaris	77.7388	325	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.7114	430	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.6962	452	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900108275.1	s__Jhaorihella thermophila	77.6136	407	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210165.1	s__CAU-1492 sp002210165	77.6133	396	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	77.5488	351	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	77.5161	412	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	77.4952	356	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	77.4084	372	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.8443	202	1618	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:48,885] [INFO] GTDB search result was written to GCF_007923355.1_ASM792335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:48,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:48,897] [INFO] DFAST_QC result json was written to GCF_007923355.1_ASM792335v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:48,897] [INFO] DFAST_QC completed!
[2024-01-24 14:56:48,897] [INFO] Total running time: 0h1m52s