[2024-01-24 12:31:57,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:57,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:57,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference
[2024-01-24 12:31:58,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:58,815] [INFO] Task started: Prodigal
[2024-01-24 12:31:58,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg38c0d7d1-9c30-4487-bb7b-cbd1689aa32c/GCF_004923205.2_ASM492320v2_genomic.fna.gz | prodigal -d GCF_004923205.2_ASM492320v2_genomic.fna/cds.fna -a GCF_004923205.2_ASM492320v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:07,758] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:07,759] [INFO] Task started: HMMsearch
[2024-01-24 12:32:07,759] [INFO] Running command: hmmsearch --tblout GCF_004923205.2_ASM492320v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference/reference_markers.hmm GCF_004923205.2_ASM492320v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:08,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:08,023] [INFO] Found 6/6 markers.
[2024-01-24 12:32:08,054] [INFO] Query marker FASTA was written to GCF_004923205.2_ASM492320v2_genomic.fna/markers.fasta
[2024-01-24 12:32:08,054] [INFO] Task started: Blastn
[2024-01-24 12:32:08,054] [INFO] Running command: blastn -query GCF_004923205.2_ASM492320v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference/reference_markers.fasta -out GCF_004923205.2_ASM492320v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:09,124] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:09,127] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:09,127] [INFO] Target genome list was writen to GCF_004923205.2_ASM492320v2_genomic.fna/target_genomes.txt
[2024-01-24 12:32:09,132] [INFO] Task started: fastANI
[2024-01-24 12:32:09,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c0d7d1-9c30-4487-bb7b-cbd1689aa32c/GCF_004923205.2_ASM492320v2_genomic.fna.gz --refList GCF_004923205.2_ASM492320v2_genomic.fna/target_genomes.txt --output GCF_004923205.2_ASM492320v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:19,453] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:19,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:19,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:19,465] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:19,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:19,465] [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 aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	100.0	1071	1075	95	conclusive
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	82.4859	619	1075	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	82.4671	655	1075	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	82.3766	641	1075	95	below_threshold
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	82.3363	641	1075	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	82.0468	656	1075	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	81.9271	626	1075	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	81.4613	568	1075	95	below_threshold
Paracoccus contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	81.046	552	1075	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	80.2264	527	1075	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.9556	545	1075	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.4516	418	1075	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.2825	428	1075	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.0009	347	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:19,467] [INFO] DFAST Taxonomy check result was written to GCF_004923205.2_ASM492320v2_genomic.fna/tc_result.tsv
[2024-01-24 12:32:19,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:19,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:19,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference/checkm_data
[2024-01-24 12:32:19,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:19,504] [INFO] Task started: CheckM
[2024-01-24 12:32:19,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004923205.2_ASM492320v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004923205.2_ASM492320v2_genomic.fna/checkm_input GCF_004923205.2_ASM492320v2_genomic.fna/checkm_result
[2024-01-24 12:32:53,427] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:53,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:53,449] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:53,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:53,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004923205.2_ASM492320v2_genomic.fna/markers.fasta)
[2024-01-24 12:32:53,450] [INFO] Task started: Blastn
[2024-01-24 12:32:53,450] [INFO] Running command: blastn -query GCF_004923205.2_ASM492320v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ec4162-95be-42a1-a65a-f6d9eafaab64/dqc_reference/reference_markers_gtdb.fasta -out GCF_004923205.2_ASM492320v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:55,478] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:55,482] [INFO] Selected 9 target genomes.
[2024-01-24 12:32:55,482] [INFO] Target genome list was writen to GCF_004923205.2_ASM492320v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:55,488] [INFO] Task started: fastANI
[2024-01-24 12:32:55,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c0d7d1-9c30-4487-bb7b-cbd1689aa32c/GCF_004923205.2_ASM492320v2_genomic.fna.gz --refList GCF_004923205.2_ASM492320v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004923205.2_ASM492320v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:03,018] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:03,026] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:03,027] [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_004923205.2	s__Paracoccus aeridis	100.0	1071	1075	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_007018965.1	s__Paracoccus marinus	88.0663	810	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061185.1	s__Paracoccus sp019061185	84.0575	707	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	82.4653	656	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCF_002287065.1	s__Paracoccus salipaludis	82.3644	643	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102885.1	s__Paracoccus chinensis	82.3609	639	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522155.1	s__Paracoccus luteus	82.0363	656	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286075.1	s__Paracoccus endophyticus	81.9194	627	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105555.1	s__Paracoccus contaminans	81.0473	552	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:03,028] [INFO] GTDB search result was written to GCF_004923205.2_ASM492320v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:03,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:03,034] [INFO] DFAST_QC result json was written to GCF_004923205.2_ASM492320v2_genomic.fna/dqc_result.json
[2024-01-24 12:33:03,034] [INFO] DFAST_QC completed!
[2024-01-24 12:33:03,034] [INFO] Total running time: 0h1m6s