[2024-01-24 13:01:39,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference
[2024-01-24 13:01:41,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,201] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,202] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9fa3af5-a0c3-4827-b430-77672c69486b/GCF_019431455.1_ASM1943145v1_genomic.fna.gz | prodigal -d GCF_019431455.1_ASM1943145v1_genomic.fna/cds.fna -a GCF_019431455.1_ASM1943145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:49,848] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:49,849] [INFO] Task started: HMMsearch
[2024-01-24 13:01:49,849] [INFO] Running command: hmmsearch --tblout GCF_019431455.1_ASM1943145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference/reference_markers.hmm GCF_019431455.1_ASM1943145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:50,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:50,145] [INFO] Found 6/6 markers.
[2024-01-24 13:01:50,187] [INFO] Query marker FASTA was written to GCF_019431455.1_ASM1943145v1_genomic.fna/markers.fasta
[2024-01-24 13:01:50,189] [INFO] Task started: Blastn
[2024-01-24 13:01:50,189] [INFO] Running command: blastn -query GCF_019431455.1_ASM1943145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference/reference_markers.fasta -out GCF_019431455.1_ASM1943145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:51,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:51,210] [INFO] Selected 18 target genomes.
[2024-01-24 13:01:51,210] [INFO] Target genome list was writen to GCF_019431455.1_ASM1943145v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:51,217] [INFO] Task started: fastANI
[2024-01-24 13:01:51,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9fa3af5-a0c3-4827-b430-77672c69486b/GCF_019431455.1_ASM1943145v1_genomic.fna.gz --refList GCF_019431455.1_ASM1943145v1_genomic.fna/target_genomes.txt --output GCF_019431455.1_ASM1943145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:09,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:09,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:09,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:09,903] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:09,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:09,903] [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 bogoriensis	strain=BOG6	GCA_019431455.1	242065	242065	type	True	100.0	971	975	95	conclusive
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	84.2506	664	975	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	83.292	709	975	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	83.037	691	975	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	82.9516	701	975	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	82.9105	679	975	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	82.508	650	975	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	82.3724	620	975	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	82.2463	662	975	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.7884	579	975	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	81.7473	637	975	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	81.4747	570	975	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.4638	592	975	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.4122	593	975	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	80.6923	587	975	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.6252	559	975	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	80.1381	480	975	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3099	460	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:09,905] [INFO] DFAST Taxonomy check result was written to GCF_019431455.1_ASM1943145v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:09,905] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:09,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:09,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference/checkm_data
[2024-01-24 13:02:09,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:09,943] [INFO] Task started: CheckM
[2024-01-24 13:02:09,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019431455.1_ASM1943145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019431455.1_ASM1943145v1_genomic.fna/checkm_input GCF_019431455.1_ASM1943145v1_genomic.fna/checkm_result
[2024-01-24 13:02:44,722] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:44,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,750] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:44,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:44,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019431455.1_ASM1943145v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:44,752] [INFO] Task started: Blastn
[2024-01-24 13:02:44,752] [INFO] Running command: blastn -query GCF_019431455.1_ASM1943145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bb5720a-73c6-47f4-91ec-863d69ec5d2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019431455.1_ASM1943145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:46,572] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:46,576] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:46,576] [INFO] Target genome list was writen to GCF_019431455.1_ASM1943145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:46,589] [INFO] Task started: fastANI
[2024-01-24 13:02:46,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9fa3af5-a0c3-4827-b430-77672c69486b/GCF_019431455.1_ASM1943145v1_genomic.fna.gz --refList GCF_019431455.1_ASM1943145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019431455.1_ASM1943145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:00,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:00,732] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:03:00,733] [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_003594815.1	s__Paracoccus aestuarii	84.2704	662	975	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	83.2829	710	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_005048225.1	s__Paracoccus gahaiensis	83.0247	692	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683865.2	s__Paracoccus liaowanqingii	82.9953	697	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_900102505.1	s__Paracoccus tibetensis	82.8487	685	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151785.1	s__Paracoccus marcusii	82.6329	618	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_000787695.1	s__Paracoccus sp000787695	82.4103	588	975	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	82.3482	623	975	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	82.2045	665	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_003255745.1	s__Paracoccus saliphilus_A	81.9172	626	975	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	81.9055	625	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259195.1	s__Paracoccus sediminilitoris	81.7285	639	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_900631945.1	s__Paracoccus haematequi	81.6847	599	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869875.1	s__Paracoccus sp016869875	81.5321	463	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	81.4639	570	975	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	81.452	593	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_018860165.1	s__Paracoccus sp018860165	81.3318	615	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111675.1	s__Paracoccus homiensis	80.7147	584	975	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 13:03:00,734] [INFO] GTDB search result was written to GCF_019431455.1_ASM1943145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:00,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:00,740] [INFO] DFAST_QC result json was written to GCF_019431455.1_ASM1943145v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:00,740] [INFO] DFAST_QC completed!
[2024-01-24 13:03:00,741] [INFO] Total running time: 0h1m21s