[2024-01-24 15:11:10,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:10,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:10,858] [INFO] DQC Reference Directory: /var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference
[2024-01-24 15:11:12,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:12,191] [INFO] Task started: Prodigal
[2024-01-24 15:11:12,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg662214d8-a703-4d3a-8143-5831b8297af3/GCF_004310345.1_ASM431034v1_genomic.fna.gz | prodigal -d GCF_004310345.1_ASM431034v1_genomic.fna/cds.fna -a GCF_004310345.1_ASM431034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:22,072] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:22,072] [INFO] Task started: HMMsearch
[2024-01-24 15:11:22,072] [INFO] Running command: hmmsearch --tblout GCF_004310345.1_ASM431034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference/reference_markers.hmm GCF_004310345.1_ASM431034v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:22,338] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:22,339] [INFO] Found 6/6 markers.
[2024-01-24 15:11:22,374] [INFO] Query marker FASTA was written to GCF_004310345.1_ASM431034v1_genomic.fna/markers.fasta
[2024-01-24 15:11:22,374] [INFO] Task started: Blastn
[2024-01-24 15:11:22,374] [INFO] Running command: blastn -query GCF_004310345.1_ASM431034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference/reference_markers.fasta -out GCF_004310345.1_ASM431034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:23,432] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:23,437] [INFO] Selected 13 target genomes.
[2024-01-24 15:11:23,437] [INFO] Target genome list was writen to GCF_004310345.1_ASM431034v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:23,444] [INFO] Task started: fastANI
[2024-01-24 15:11:23,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg662214d8-a703-4d3a-8143-5831b8297af3/GCF_004310345.1_ASM431034v1_genomic.fna.gz --refList GCF_004310345.1_ASM431034v1_genomic.fna/target_genomes.txt --output GCF_004310345.1_ASM431034v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:35,016] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:35,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:35,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:35,033] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:35,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:35,033] [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 subflavus	strain=GY0581	GCA_004310345.1	2528244	2528244	type	True	100.0	1046	1049	95	conclusive
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	85.7443	750	1049	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	85.6634	762	1049	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	85.6596	756	1049	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	85.5692	760	1049	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	85.2077	748	1049	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	84.9849	723	1049	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	84.83	691	1049	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	84.6276	717	1049	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	84.6007	724	1049	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.2331	597	1049	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.9801	549	1049	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3216	474	1049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:35,035] [INFO] DFAST Taxonomy check result was written to GCF_004310345.1_ASM431034v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:35,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:35,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:35,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference/checkm_data
[2024-01-24 15:11:35,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:35,072] [INFO] Task started: CheckM
[2024-01-24 15:11:35,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310345.1_ASM431034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310345.1_ASM431034v1_genomic.fna/checkm_input GCF_004310345.1_ASM431034v1_genomic.fna/checkm_result
[2024-01-24 15:12:09,139] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:09,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:09,161] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:09,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:09,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310345.1_ASM431034v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:09,162] [INFO] Task started: Blastn
[2024-01-24 15:12:09,162] [INFO] Running command: blastn -query GCF_004310345.1_ASM431034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967ed7b7-f734-4101-8ccd-b628f1fb7b24/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310345.1_ASM431034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:11,144] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:11,153] [INFO] Selected 8 target genomes.
[2024-01-24 15:12:11,154] [INFO] Target genome list was writen to GCF_004310345.1_ASM431034v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:11,177] [INFO] Task started: fastANI
[2024-01-24 15:12:11,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg662214d8-a703-4d3a-8143-5831b8297af3/GCF_004310345.1_ASM431034v1_genomic.fna.gz --refList GCF_004310345.1_ASM431034v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310345.1_ASM431034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:18,632] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:18,647] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:18,647] [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_004310345.1	s__Paracoccus subflavus	100.0	1046	1049	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_900188295.1	s__Paracoccus sediminis	85.6781	761	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009708075.1	s__Paracoccus lichenicola	85.6544	756	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315735.1	s__Paracoccus sp017315735	85.5828	758	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	85.2895	757	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642735.1	s__Paracoccus acridae	85.1933	749	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_017356265.1	s__Paracoccus fontiphilus	84.9859	723	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	84.5867	725	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:18,649] [INFO] GTDB search result was written to GCF_004310345.1_ASM431034v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:18,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:18,653] [INFO] DFAST_QC result json was written to GCF_004310345.1_ASM431034v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:18,653] [INFO] DFAST_QC completed!
[2024-01-24 15:12:18,653] [INFO] Total running time: 0h1m8s