[2024-01-24 13:59:42,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:59:42,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:59:42,823] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference
[2024-01-24 13:59:44,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:59:44,068] [INFO] Task started: Prodigal
[2024-01-24 13:59:44,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg3202864d-60cd-4a71-91b9-53b6b986b95f/GCF_007004645.1_ASM700464v1_genomic.fna.gz | prodigal -d GCF_007004645.1_ASM700464v1_genomic.fna/cds.fna -a GCF_007004645.1_ASM700464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:54,889] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:54,889] [INFO] Task started: HMMsearch
[2024-01-24 13:59:54,890] [INFO] Running command: hmmsearch --tblout GCF_007004645.1_ASM700464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference/reference_markers.hmm GCF_007004645.1_ASM700464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:55,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:55,142] [INFO] Found 6/6 markers.
[2024-01-24 13:59:55,174] [INFO] Query marker FASTA was written to GCF_007004645.1_ASM700464v1_genomic.fna/markers.fasta
[2024-01-24 13:59:55,174] [INFO] Task started: Blastn
[2024-01-24 13:59:55,174] [INFO] Running command: blastn -query GCF_007004645.1_ASM700464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference/reference_markers.fasta -out GCF_007004645.1_ASM700464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:55,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:56,000] [INFO] Selected 15 target genomes.
[2024-01-24 13:59:56,000] [INFO] Target genome list was writen to GCF_007004645.1_ASM700464v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:56,005] [INFO] Task started: fastANI
[2024-01-24 13:59:56,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg3202864d-60cd-4a71-91b9-53b6b986b95f/GCF_007004645.1_ASM700464v1_genomic.fna.gz --refList GCF_007004645.1_ASM700464v1_genomic.fna/target_genomes.txt --output GCF_007004645.1_ASM700464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:00:05,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:05,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:00:05,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:00:05,881] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:00:05,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:00:05,881] [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 halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	100.0	1115	1117	95	conclusive
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	84.4492	754	1117	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	83.8112	778	1117	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	79.4614	520	1117	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	79.0273	483	1117	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	78.8711	407	1117	95	below_threshold
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	78.8535	411	1117	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.7177	273	1117	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.7076	250	1117	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	77.3166	216	1117	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.105	159	1117	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.0952	160	1117	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.9107	159	1117	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.7428	172	1117	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.7428	172	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:00:05,883] [INFO] DFAST Taxonomy check result was written to GCF_007004645.1_ASM700464v1_genomic.fna/tc_result.tsv
[2024-01-24 14:00:05,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:00:05,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:00:05,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference/checkm_data
[2024-01-24 14:00:05,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:00:05,918] [INFO] Task started: CheckM
[2024-01-24 14:00:05,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004645.1_ASM700464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004645.1_ASM700464v1_genomic.fna/checkm_input GCF_007004645.1_ASM700464v1_genomic.fna/checkm_result
[2024-01-24 14:00:41,688] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:41,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:41,706] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:41,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:41,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004645.1_ASM700464v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:41,707] [INFO] Task started: Blastn
[2024-01-24 14:00:41,707] [INFO] Running command: blastn -query GCF_007004645.1_ASM700464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4190541-dd56-4af6-937a-b4552a61ea72/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004645.1_ASM700464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:43,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:43,170] [INFO] Selected 9 target genomes.
[2024-01-24 14:00:43,170] [INFO] Target genome list was writen to GCF_007004645.1_ASM700464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:43,173] [INFO] Task started: fastANI
[2024-01-24 14:00:43,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg3202864d-60cd-4a71-91b9-53b6b986b95f/GCF_007004645.1_ASM700464v1_genomic.fna.gz --refList GCF_007004645.1_ASM700464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004645.1_ASM700464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:49,718] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:49,726] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:49,726] [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_007004645.1	s__Aliiroseovarius halocynthiae	100.0	1115	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004360145.1	s__Aliiroseovarius marinus	84.4492	754	1117	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	84.1527	775	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	83.8094	779	1117	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	79.4707	519	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109955.1	s__Aliiroseovarius sediminilitoris	79.0273	483	1117	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	78.8916	405	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	-
GCF_017743735.1	s__Shimia sp017743735	77.1851	241	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_009711265.1	s__Paracoccus sp009711265	77.0286	163	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:49,728] [INFO] GTDB search result was written to GCF_007004645.1_ASM700464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:49,728] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:49,731] [INFO] DFAST_QC result json was written to GCF_007004645.1_ASM700464v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:49,732] [INFO] DFAST_QC completed!
[2024-01-24 14:00:49,732] [INFO] Total running time: 0h1m7s