[2024-01-24 12:46:54,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:54,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:54,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference
[2024-01-24 12:46:56,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:56,082] [INFO] Task started: Prodigal
[2024-01-24 12:46:56,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbbf409b-922d-43ba-92f5-4279f153495b/GCF_005887635.2_ASM588763v2_genomic.fna.gz | prodigal -d GCF_005887635.2_ASM588763v2_genomic.fna/cds.fna -a GCF_005887635.2_ASM588763v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:12,624] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:12,625] [INFO] Task started: HMMsearch
[2024-01-24 12:47:12,625] [INFO] Running command: hmmsearch --tblout GCF_005887635.2_ASM588763v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference/reference_markers.hmm GCF_005887635.2_ASM588763v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:12,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:12,955] [INFO] Found 6/6 markers.
[2024-01-24 12:47:13,004] [INFO] Query marker FASTA was written to GCF_005887635.2_ASM588763v2_genomic.fna/markers.fasta
[2024-01-24 12:47:13,004] [INFO] Task started: Blastn
[2024-01-24 12:47:13,004] [INFO] Running command: blastn -query GCF_005887635.2_ASM588763v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference/reference_markers.fasta -out GCF_005887635.2_ASM588763v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:13,973] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:13,976] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:13,977] [INFO] Target genome list was writen to GCF_005887635.2_ASM588763v2_genomic.fna/target_genomes.txt
[2024-01-24 12:47:13,985] [INFO] Task started: fastANI
[2024-01-24 12:47:13,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbf409b-922d-43ba-92f5-4279f153495b/GCF_005887635.2_ASM588763v2_genomic.fna.gz --refList GCF_005887635.2_ASM588763v2_genomic.fna/target_genomes.txt --output GCF_005887635.2_ASM588763v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:35,544] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:35,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:35,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:35,562] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:35,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:35,562] [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
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	100.0	1817	1820	95	conclusive
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	78.3169	505	1820	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.2968	463	1820	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.2789	522	1820	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	78.271	709	1820	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	78.1633	613	1820	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.1012	587	1820	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	78.0642	442	1820	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	77.9692	447	1820	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.9147	379	1820	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	77.9086	437	1820	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.7854	413	1820	95	below_threshold
Thermohalobaculum xanthum	strain=M0105	GCA_016623495.1	2753746	2753746	type	True	77.7341	431	1820	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.6792	512	1820	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	77.4866	547	1820	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.4749	470	1820	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.4675	513	1820	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.4352	477	1820	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	77.3036	385	1820	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	77.1682	390	1820	95	below_threshold
Pikeienuella piscinae	strain=RR4-56	GCA_011044155.1	2748098	2748098	type	True	77.0692	355	1820	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.7428	261	1820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:35,564] [INFO] DFAST Taxonomy check result was written to GCF_005887635.2_ASM588763v2_genomic.fna/tc_result.tsv
[2024-01-24 12:47:35,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:35,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:35,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference/checkm_data
[2024-01-24 12:47:35,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:35,627] [INFO] Task started: CheckM
[2024-01-24 12:47:35,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005887635.2_ASM588763v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005887635.2_ASM588763v2_genomic.fna/checkm_input GCF_005887635.2_ASM588763v2_genomic.fna/checkm_result
[2024-01-24 12:48:57,070] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:57,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,092] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:57,092] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:57,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005887635.2_ASM588763v2_genomic.fna/markers.fasta)
[2024-01-24 12:48:57,093] [INFO] Task started: Blastn
[2024-01-24 12:48:57,093] [INFO] Running command: blastn -query GCF_005887635.2_ASM588763v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg100828c0-705b-45da-ab3e-9d41eb5ab9cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_005887635.2_ASM588763v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:58,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:58,819] [INFO] Selected 20 target genomes.
[2024-01-24 12:48:58,819] [INFO] Target genome list was writen to GCF_005887635.2_ASM588763v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:58,835] [INFO] Task started: fastANI
[2024-01-24 12:48:58,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbf409b-922d-43ba-92f5-4279f153495b/GCF_005887635.2_ASM588763v2_genomic.fna.gz --refList GCF_005887635.2_ASM588763v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005887635.2_ASM588763v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:17,939] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:17,961] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:17,961] [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_005887635.2	s__Paroceanicella profunda	100.0	1818	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003448965.1	s__Paroceanicella sp003448965	89.3157	1438	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013093415.1	s__Halovulum dunhuangense	78.3613	453	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	78.3383	504	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113695.1	s__Albimonas pacifica	78.2797	708	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	78.2563	524	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_900106695.1	s__Albimonas donghaensis	78.2007	608	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_000153305.1	s__Oceanicola granulosus	78.1587	473	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	78.1559	578	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290545.1	s__Monaibacterium sp011290545	78.1558	255	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	96.75	96.75	0.88	0.88	2	-
GCA_003241785.1	s__Amaricoccus sp003241785	77.9793	526	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018145.1	s__Dinoroseobacter shibae	77.8814	381	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	77.7721	385	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385555.1	s__Rhodosalinus sediminis	77.761	437	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.7241	674	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	77.6661	340	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	77.6659	514	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	77.442	517	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006152145.1	s__Rubellimicrobium roseum	77.3106	384	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022215.1	s__Paenirhodobacter populi	76.9332	345	1820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:17,962] [INFO] GTDB search result was written to GCF_005887635.2_ASM588763v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:17,963] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:17,967] [INFO] DFAST_QC result json was written to GCF_005887635.2_ASM588763v2_genomic.fna/dqc_result.json
[2024-01-24 12:49:17,967] [INFO] DFAST_QC completed!
[2024-01-24 12:49:17,967] [INFO] Total running time: 0h2m23s