[2024-01-24 14:56:23,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference
[2024-01-24 14:56:26,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,557] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg2457cf75-5885-43f5-995a-404af5294bfc/GCF_014642495.1_ASM1464249v1_genomic.fna.gz | prodigal -d GCF_014642495.1_ASM1464249v1_genomic.fna/cds.fna -a GCF_014642495.1_ASM1464249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:36,808] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:36,809] [INFO] Task started: HMMsearch
[2024-01-24 14:56:36,809] [INFO] Running command: hmmsearch --tblout GCF_014642495.1_ASM1464249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference/reference_markers.hmm GCF_014642495.1_ASM1464249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:37,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:37,212] [INFO] Found 6/6 markers.
[2024-01-24 14:56:37,243] [INFO] Query marker FASTA was written to GCF_014642495.1_ASM1464249v1_genomic.fna/markers.fasta
[2024-01-24 14:56:37,244] [INFO] Task started: Blastn
[2024-01-24 14:56:37,244] [INFO] Running command: blastn -query GCF_014642495.1_ASM1464249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference/reference_markers.fasta -out GCF_014642495.1_ASM1464249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:38,264] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:38,269] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:38,269] [INFO] Target genome list was writen to GCF_014642495.1_ASM1464249v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:38,286] [INFO] Task started: fastANI
[2024-01-24 14:56:38,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg2457cf75-5885-43f5-995a-404af5294bfc/GCF_014642495.1_ASM1464249v1_genomic.fna.gz --refList GCF_014642495.1_ASM1464249v1_genomic.fna/target_genomes.txt --output GCF_014642495.1_ASM1464249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:48,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:48,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:48,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:48,264] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:48,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:48,264] [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 pelagius	strain=CGMCC 1.15358	GCA_014642495.1	1703341	1703341	type	True	100.0	1055	1056	95	conclusive
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	99.9979	1052	1056	95	conclusive
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	89.7471	851	1056	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	86.746	812	1056	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	83.1869	638	1056	95	below_threshold
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	81.8994	615	1056	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.354	334	1056	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	79.3016	365	1056	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.6545	352	1056	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.465	232	1056	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.2713	307	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:48,266] [INFO] DFAST Taxonomy check result was written to GCF_014642495.1_ASM1464249v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:48,266] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:48,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:48,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference/checkm_data
[2024-01-24 14:56:48,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:48,308] [INFO] Task started: CheckM
[2024-01-24 14:56:48,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642495.1_ASM1464249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642495.1_ASM1464249v1_genomic.fna/checkm_input GCF_014642495.1_ASM1464249v1_genomic.fna/checkm_result
[2024-01-24 14:57:21,342] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:21,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:21,363] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:21,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:21,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642495.1_ASM1464249v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:21,365] [INFO] Task started: Blastn
[2024-01-24 14:57:21,365] [INFO] Running command: blastn -query GCF_014642495.1_ASM1464249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebb36ad-f6fd-411a-a0ec-6bbf478d2c69/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642495.1_ASM1464249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:23,097] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:23,104] [INFO] Selected 9 target genomes.
[2024-01-24 14:57:23,104] [INFO] Target genome list was writen to GCF_014642495.1_ASM1464249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:23,118] [INFO] Task started: fastANI
[2024-01-24 14:57:23,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg2457cf75-5885-43f5-995a-404af5294bfc/GCF_014642495.1_ASM1464249v1_genomic.fna.gz --refList GCF_014642495.1_ASM1464249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642495.1_ASM1464249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:30,787] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:30,798] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:30,799] [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_001661915.1	s__Croceicoccus pelagius	99.9979	1052	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018398395.1	s__Croceicoccus sp018398395	89.7242	853	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570835.1	s__Croceicoccus sediminis	86.746	812	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634625.1	s__Croceicoccus bisphenolivorans	83.2009	637	1056	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	81.8637	620	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004004515.1	s__Croceicoccus ponticola	80.8006	590	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661965.1	s__Croceicoccus mobilis	80.0958	510	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018417475.1	s__Novosphingobium sp000813185	78.9663	348	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_018491765.1	s__Novosphingobium profundi	78.6372	354	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:30,801] [INFO] GTDB search result was written to GCF_014642495.1_ASM1464249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:30,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:30,805] [INFO] DFAST_QC result json was written to GCF_014642495.1_ASM1464249v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:30,805] [INFO] DFAST_QC completed!
[2024-01-24 14:57:30,805] [INFO] Total running time: 0h1m7s