[2024-01-24 12:31:04,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference
[2024-01-24 12:31:05,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,934] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,934] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2e7a528-900e-400c-8556-d92a9a4614a9/GCF_003056335.1_ASM305633v1_genomic.fna.gz | prodigal -d GCF_003056335.1_ASM305633v1_genomic.fna/cds.fna -a GCF_003056335.1_ASM305633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:16,670] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:16,670] [INFO] Task started: HMMsearch
[2024-01-24 12:31:16,670] [INFO] Running command: hmmsearch --tblout GCF_003056335.1_ASM305633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference/reference_markers.hmm GCF_003056335.1_ASM305633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:16,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:16,951] [INFO] Found 6/6 markers.
[2024-01-24 12:31:17,003] [INFO] Query marker FASTA was written to GCF_003056335.1_ASM305633v1_genomic.fna/markers.fasta
[2024-01-24 12:31:17,004] [INFO] Task started: Blastn
[2024-01-24 12:31:17,004] [INFO] Running command: blastn -query GCF_003056335.1_ASM305633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference/reference_markers.fasta -out GCF_003056335.1_ASM305633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:18,151] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:18,155] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:18,155] [INFO] Target genome list was writen to GCF_003056335.1_ASM305633v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:18,171] [INFO] Task started: fastANI
[2024-01-24 12:31:18,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e7a528-900e-400c-8556-d92a9a4614a9/GCF_003056335.1_ASM305633v1_genomic.fna.gz --refList GCF_003056335.1_ASM305633v1_genomic.fna/target_genomes.txt --output GCF_003056335.1_ASM305633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:31,258] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:31,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:31,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:31,271] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:31,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:31,272] [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
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	100.0	1152	1153	95	conclusive
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	89.4965	911	1153	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	83.7611	706	1153	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	83.7458	810	1153	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	83.7294	792	1153	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	83.5265	741	1153	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	82.8208	757	1153	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	82.1212	710	1153	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	82.0253	665	1153	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.723	660	1153	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.4551	659	1153	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.4321	668	1153	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.2015	592	1153	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.6564	603	1153	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3654	503	1153	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:31,273] [INFO] DFAST Taxonomy check result was written to GCF_003056335.1_ASM305633v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:31,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:31,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:31,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference/checkm_data
[2024-01-24 12:31:31,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:31,314] [INFO] Task started: CheckM
[2024-01-24 12:31:31,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003056335.1_ASM305633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003056335.1_ASM305633v1_genomic.fna/checkm_input GCF_003056335.1_ASM305633v1_genomic.fna/checkm_result
[2024-01-24 12:32:11,861] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:11,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,886] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:11,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:11,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003056335.1_ASM305633v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:11,887] [INFO] Task started: Blastn
[2024-01-24 12:32:11,887] [INFO] Running command: blastn -query GCF_003056335.1_ASM305633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa72f96e-6575-4001-94aa-052267761626/dqc_reference/reference_markers_gtdb.fasta -out GCF_003056335.1_ASM305633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:13,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:13,818] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:13,818] [INFO] Target genome list was writen to GCF_003056335.1_ASM305633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:13,828] [INFO] Task started: fastANI
[2024-01-24 12:32:13,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e7a528-900e-400c-8556-d92a9a4614a9/GCF_003056335.1_ASM305633v1_genomic.fna.gz --refList GCF_003056335.1_ASM305633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003056335.1_ASM305633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:23,027] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,041] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:23,042] [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_003056335.1	s__Paracoccus indicus	100.0	1152	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003259195.1	s__Paracoccus sediminilitoris	89.4725	913	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_003590715.1	s__Paracoccus sp003590715	83.9121	786	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048265.1	s__Paracoccus hibiscisoli	83.7692	788	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_004683865.2	s__Paracoccus liaowanqingii	83.7572	809	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_006151785.1	s__Paracoccus marcusii	83.7516	720	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_003594815.1	s__Paracoccus aestuarii	83.748	707	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	83.5022	743	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787695.1	s__Paracoccus sp000787695	83.4992	694	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860625.1	s__Paracoccus sp018860625	83.2778	752	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	82.1142	711	1153	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,043] [INFO] GTDB search result was written to GCF_003056335.1_ASM305633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:23,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:23,049] [INFO] DFAST_QC result json was written to GCF_003056335.1_ASM305633v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:23,049] [INFO] DFAST_QC completed!
[2024-01-24 12:32:23,049] [INFO] Total running time: 0h1m18s