[2024-01-24 11:05:25,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference
[2024-01-24 11:05:26,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,903] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,904] [INFO] Running command: gunzip -c /var/lib/cwl/stgf00eda32-478a-4d56-a755-0d6d3069b489/GCF_007570835.1_ASM757083v1_genomic.fna.gz | prodigal -d GCF_007570835.1_ASM757083v1_genomic.fna/cds.fna -a GCF_007570835.1_ASM757083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:37,526] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:37,526] [INFO] Task started: HMMsearch
[2024-01-24 11:05:37,527] [INFO] Running command: hmmsearch --tblout GCF_007570835.1_ASM757083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference/reference_markers.hmm GCF_007570835.1_ASM757083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:37,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:37,799] [INFO] Found 6/6 markers.
[2024-01-24 11:05:37,833] [INFO] Query marker FASTA was written to GCF_007570835.1_ASM757083v1_genomic.fna/markers.fasta
[2024-01-24 11:05:37,834] [INFO] Task started: Blastn
[2024-01-24 11:05:37,834] [INFO] Running command: blastn -query GCF_007570835.1_ASM757083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference/reference_markers.fasta -out GCF_007570835.1_ASM757083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:38,799] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:38,811] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:38,812] [INFO] Target genome list was writen to GCF_007570835.1_ASM757083v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:38,816] [INFO] Task started: fastANI
[2024-01-24 11:05:38,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgf00eda32-478a-4d56-a755-0d6d3069b489/GCF_007570835.1_ASM757083v1_genomic.fna.gz --refList GCF_007570835.1_ASM757083v1_genomic.fna/target_genomes.txt --output GCF_007570835.1_ASM757083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:47,097] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:47,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:47,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:47,114] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:47,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:47,115] [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
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	100.0	1176	1176	95	conclusive
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	87.307	796	1176	95	below_threshold
Croceicoccus pelagius	strain=CGMCC 1.15358	GCA_014642495.1	1703341	1703341	type	True	86.9132	801	1176	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	86.894	795	1176	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	82.9611	637	1176	95	below_threshold
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	82.1285	605	1176	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	79.0741	404	1176	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.7938	333	1176	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.4542	307	1176	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.362	304	1176	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.3091	338	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:47,116] [INFO] DFAST Taxonomy check result was written to GCF_007570835.1_ASM757083v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:47,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:47,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:47,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference/checkm_data
[2024-01-24 11:05:47,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:47,153] [INFO] Task started: CheckM
[2024-01-24 11:05:47,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007570835.1_ASM757083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007570835.1_ASM757083v1_genomic.fna/checkm_input GCF_007570835.1_ASM757083v1_genomic.fna/checkm_result
[2024-01-24 11:06:20,834] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:20,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:20,853] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:20,853] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:20,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007570835.1_ASM757083v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:20,854] [INFO] Task started: Blastn
[2024-01-24 11:06:20,854] [INFO] Running command: blastn -query GCF_007570835.1_ASM757083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2249311a-9422-4952-93e3-8daafd91713f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007570835.1_ASM757083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:22,600] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:22,605] [INFO] Selected 9 target genomes.
[2024-01-24 11:06:22,605] [INFO] Target genome list was writen to GCF_007570835.1_ASM757083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:22,613] [INFO] Task started: fastANI
[2024-01-24 11:06:22,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgf00eda32-478a-4d56-a755-0d6d3069b489/GCF_007570835.1_ASM757083v1_genomic.fna.gz --refList GCF_007570835.1_ASM757083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007570835.1_ASM757083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:30,331] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:30,344] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:30,344] [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_007570835.1	s__Croceicoccus sediminis	100.0	1176	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018398395.1	s__Croceicoccus sp018398395	87.2942	797	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661915.1	s__Croceicoccus pelagius	86.894	795	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001634625.1	s__Croceicoccus bisphenolivorans	82.9611	637	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028705.1	s__Croceicoccus naphthovorans	82.0954	611	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001661965.1	s__Croceicoccus mobilis	79.9626	522	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002694745.1	s__Croceicoccus sp002694745	79.8586	475	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	99.91	99.91	0.91	0.91	2	-
GCF_018491765.1	s__Novosphingobium profundi	78.794	333	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	77.9992	283	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:30,346] [INFO] GTDB search result was written to GCF_007570835.1_ASM757083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:30,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:30,351] [INFO] DFAST_QC result json was written to GCF_007570835.1_ASM757083v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:30,351] [INFO] DFAST_QC completed!
[2024-01-24 11:06:30,351] [INFO] Total running time: 0h1m5s