[2024-01-24 13:31:35,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference
[2024-01-24 13:31:36,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,738] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,738] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1454351-ac54-49b6-8530-52ceb83cd8ed/GCF_018599245.1_ASM1859924v1_genomic.fna.gz | prodigal -d GCF_018599245.1_ASM1859924v1_genomic.fna/cds.fna -a GCF_018599245.1_ASM1859924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,490] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,491] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,491] [INFO] Running command: hmmsearch --tblout GCF_018599245.1_ASM1859924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference/reference_markers.hmm GCF_018599245.1_ASM1859924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,828] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,862] [INFO] Query marker FASTA was written to GCF_018599245.1_ASM1859924v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,862] [INFO] Task started: Blastn
[2024-01-24 13:31:48,862] [INFO] Running command: blastn -query GCF_018599245.1_ASM1859924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference/reference_markers.fasta -out GCF_018599245.1_ASM1859924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,703] [INFO] Selected 21 target genomes.
[2024-01-24 13:31:49,704] [INFO] Target genome list was writen to GCF_018599245.1_ASM1859924v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,717] [INFO] Task started: fastANI
[2024-01-24 13:31:49,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1454351-ac54-49b6-8530-52ceb83cd8ed/GCF_018599245.1_ASM1859924v1_genomic.fna.gz --refList GCF_018599245.1_ASM1859924v1_genomic.fna/target_genomes.txt --output GCF_018599245.1_ASM1859924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:05,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:05,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:05,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:05,255] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:05,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:05,256] [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
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	78.7736	506	1106	95	below_threshold
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	78.7518	505	1106	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	78.2443	363	1106	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	78.1083	368	1106	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	77.9595	361	1106	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	77.7908	351	1106	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	77.7052	373	1106	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	77.3078	187	1106	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	77.2978	205	1106	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.2006	188	1106	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.0272	189	1106	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.0066	189	1106	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.774	194	1106	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.7447	141	1106	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	76.7241	148	1106	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6377	86	1106	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.5683	107	1106	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	76.5634	157	1106	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.4273	103	1106	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.1468	147	1106	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.0413	104	1106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:05,258] [INFO] DFAST Taxonomy check result was written to GCF_018599245.1_ASM1859924v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:05,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:05,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:05,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference/checkm_data
[2024-01-24 13:32:05,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:05,295] [INFO] Task started: CheckM
[2024-01-24 13:32:05,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018599245.1_ASM1859924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018599245.1_ASM1859924v1_genomic.fna/checkm_input GCF_018599245.1_ASM1859924v1_genomic.fna/checkm_result
[2024-01-24 13:32:44,375] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:44,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:44,392] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:44,392] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:44,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018599245.1_ASM1859924v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:44,393] [INFO] Task started: Blastn
[2024-01-24 13:32:44,393] [INFO] Running command: blastn -query GCF_018599245.1_ASM1859924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b6dff62-342c-477a-905c-246842e9b38d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018599245.1_ASM1859924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:45,451] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:45,454] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:45,454] [INFO] Target genome list was writen to GCF_018599245.1_ASM1859924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:45,466] [INFO] Task started: fastANI
[2024-01-24 13:32:45,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1454351-ac54-49b6-8530-52ceb83cd8ed/GCF_018599245.1_ASM1859924v1_genomic.fna.gz --refList GCF_018599245.1_ASM1859924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018599245.1_ASM1859924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:54,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:54,615] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:54,616] [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_018599245.1	s__Aliiroseovarius lamellibrachiae	100.0	1106	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002340515.1	s__Aliiroseovarius sp002340515	89.5632	816	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307765.1	s__Aliiroseovarius crassostreae	78.7947	503	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	78.2343	364	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	78.1554	374	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	78.1177	367	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004645.1	s__Aliiroseovarius halocynthiae	77.9691	360	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656375.1	s__Aliiroseovarius zhejiangensis	77.7052	373	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	77.338	185	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	77.2978	205	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458175.1	s__Shimia marina	77.0272	189	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_011806455.1	s__Celeribacter sp011806455	76.8555	153	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCA_002708925.1	s__Thalassobius sp002708925	76.7018	171	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:54,618] [INFO] GTDB search result was written to GCF_018599245.1_ASM1859924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:54,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:54,631] [INFO] DFAST_QC result json was written to GCF_018599245.1_ASM1859924v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:54,631] [INFO] DFAST_QC completed!
[2024-01-24 13:32:54,631] [INFO] Total running time: 0h1m19s