[2024-01-25 18:48:05,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:05,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:05,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference
[2024-01-25 18:48:06,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:06,744] [INFO] Task started: Prodigal
[2024-01-25 18:48:06,744] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0fc1e15-8b63-4aae-b30e-a3dc541767b0/GCF_003709565.1_ASM370956v1_genomic.fna.gz | prodigal -d GCF_003709565.1_ASM370956v1_genomic.fna/cds.fna -a GCF_003709565.1_ASM370956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:18,563] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:18,563] [INFO] Task started: HMMsearch
[2024-01-25 18:48:18,563] [INFO] Running command: hmmsearch --tblout GCF_003709565.1_ASM370956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference/reference_markers.hmm GCF_003709565.1_ASM370956v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:18,833] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:18,834] [INFO] Found 6/6 markers.
[2024-01-25 18:48:18,872] [INFO] Query marker FASTA was written to GCF_003709565.1_ASM370956v1_genomic.fna/markers.fasta
[2024-01-25 18:48:18,873] [INFO] Task started: Blastn
[2024-01-25 18:48:18,873] [INFO] Running command: blastn -query GCF_003709565.1_ASM370956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference/reference_markers.fasta -out GCF_003709565.1_ASM370956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:19,874] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:19,877] [INFO] Selected 19 target genomes.
[2024-01-25 18:48:19,878] [INFO] Target genome list was writen to GCF_003709565.1_ASM370956v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:19,895] [INFO] Task started: fastANI
[2024-01-25 18:48:19,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fc1e15-8b63-4aae-b30e-a3dc541767b0/GCF_003709565.1_ASM370956v1_genomic.fna.gz --refList GCF_003709565.1_ASM370956v1_genomic.fna/target_genomes.txt --output GCF_003709565.1_ASM370956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:38,062] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:38,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:38,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:38,074] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:48:38,074] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:38,074] [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 siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	100.0	1572	1577	95	conclusive
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	99.9058	1462	1577	95	conclusive
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	85.5364	984	1577	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	83.5971	858	1577	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	83.5383	793	1577	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	83.5058	700	1577	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	83.4569	777	1577	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	83.4472	745	1577	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	83.1875	761	1577	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	83.1586	770	1577	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	83.0705	769	1577	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	82.8929	692	1577	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	82.2727	677	1577	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	82.2359	816	1577	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	82.1653	719	1577	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	82.0351	752	1577	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	82.0068	799	1577	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.866	755	1577	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.6162	628	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:38,076] [INFO] DFAST Taxonomy check result was written to GCF_003709565.1_ASM370956v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:38,076] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:38,076] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:38,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference/checkm_data
[2024-01-25 18:48:38,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:38,123] [INFO] Task started: CheckM
[2024-01-25 18:48:38,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003709565.1_ASM370956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003709565.1_ASM370956v1_genomic.fna/checkm_input GCF_003709565.1_ASM370956v1_genomic.fna/checkm_result
[2024-01-25 18:49:33,512] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:33,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:33,534] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:33,534] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:33,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003709565.1_ASM370956v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:33,535] [INFO] Task started: Blastn
[2024-01-25 18:49:33,535] [INFO] Running command: blastn -query GCF_003709565.1_ASM370956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bc20cb6-38cb-4fb3-b009-4afb8f6ba437/dqc_reference/reference_markers_gtdb.fasta -out GCF_003709565.1_ASM370956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:35,660] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:35,663] [INFO] Selected 19 target genomes.
[2024-01-25 18:49:35,664] [INFO] Target genome list was writen to GCF_003709565.1_ASM370956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:35,683] [INFO] Task started: fastANI
[2024-01-25 18:49:35,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fc1e15-8b63-4aae-b30e-a3dc541767b0/GCF_003709565.1_ASM370956v1_genomic.fna.gz --refList GCF_003709565.1_ASM370956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003709565.1_ASM370956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:55,100] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:55,112] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:55,113] [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_003709565.1	s__Paracoccus siganidrum	100.0	1572	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_900110285.1	s__Paracoccus alcaliphilus	85.5434	983	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	84.2204	794	1577	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	84.0108	809	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	83.6387	866	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_016446475.1	s__Paracoccus binzhouensis	83.6224	857	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594815.1	s__Paracoccus aestuarii	83.5127	699	1577	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	83.5091	795	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708075.1	s__Paracoccus lichenicola	83.4837	743	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	83.2574	851	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_014642735.1	s__Paracoccus acridae	83.1628	770	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	82.9068	690	1577	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	82.4345	689	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_018860625.1	s__Paracoccus sp018860625	82.3808	667	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007735.2	s__Paracoccus marinus_A	82.2901	750	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	82.2738	812	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622145.1	s__Paracoccus yeei	82.0366	794	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_017744015.1	s__Paracoccus sp002732665	81.8538	727	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_003697785.1	s__Paracoccus alkanivorans	81.6069	743	1577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:55,114] [INFO] GTDB search result was written to GCF_003709565.1_ASM370956v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:55,116] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:55,119] [INFO] DFAST_QC result json was written to GCF_003709565.1_ASM370956v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:55,120] [INFO] DFAST_QC completed!
[2024-01-25 18:49:55,120] [INFO] Total running time: 0h1m50s