[2024-01-24 13:45:46,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference
[2024-01-24 13:45:47,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,785] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg408dd169-9b34-46d9-8045-9d3a2c93e87c/GCF_014235845.1_ASM1423584v1_genomic.fna.gz | prodigal -d GCF_014235845.1_ASM1423584v1_genomic.fna/cds.fna -a GCF_014235845.1_ASM1423584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:01,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:01,841] [INFO] Task started: HMMsearch
[2024-01-24 13:46:01,841] [INFO] Running command: hmmsearch --tblout GCF_014235845.1_ASM1423584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference/reference_markers.hmm GCF_014235845.1_ASM1423584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:02,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:02,200] [INFO] Found 6/6 markers.
[2024-01-24 13:46:02,254] [INFO] Query marker FASTA was written to GCF_014235845.1_ASM1423584v1_genomic.fna/markers.fasta
[2024-01-24 13:46:02,254] [INFO] Task started: Blastn
[2024-01-24 13:46:02,254] [INFO] Running command: blastn -query GCF_014235845.1_ASM1423584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference/reference_markers.fasta -out GCF_014235845.1_ASM1423584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:03,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:03,254] [INFO] Selected 28 target genomes.
[2024-01-24 13:46:03,254] [INFO] Target genome list was writen to GCF_014235845.1_ASM1423584v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:03,279] [INFO] Task started: fastANI
[2024-01-24 13:46:03,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg408dd169-9b34-46d9-8045-9d3a2c93e87c/GCF_014235845.1_ASM1423584v1_genomic.fna.gz --refList GCF_014235845.1_ASM1423584v1_genomic.fna/target_genomes.txt --output GCF_014235845.1_ASM1423584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:24,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:24,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:24,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:24,131] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:24,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:24,131] [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
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.833	206	1163	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	78.6032	431	1163	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.4775	221	1163	95	below_threshold
Pontivivens insulae	strain=CeCT 8812	GCA_900302495.1	1639689	1639689	type	True	78.2196	291	1163	95	below_threshold
Pontivivens insulae	strain=DSM 103361	GCA_003385715.1	1639689	1639689	type	True	78.1891	294	1163	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.998	208	1163	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.7026	227	1163	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.6984	233	1163	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.659	257	1163	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	77.5423	186	1163	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.5121	278	1163	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	77.3161	220	1163	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3004	213	1163	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.1513	196	1163	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.1306	169	1163	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	77.1136	199	1163	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.0801	219	1163	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.001	172	1163	95	below_threshold
Paracoccus xiamenensis	strain=12-3	GCA_011308835.1	2714901	2714901	type	True	76.9916	156	1163	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.943	181	1163	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	76.9172	145	1163	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	76.9109	172	1163	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.9098	236	1163	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.8948	191	1163	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	76.8868	173	1163	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	76.8853	174	1163	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.8175	211	1163	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	76.7915	140	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:24,140] [INFO] DFAST Taxonomy check result was written to GCF_014235845.1_ASM1423584v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:24,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:24,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:24,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference/checkm_data
[2024-01-24 13:46:24,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:24,203] [INFO] Task started: CheckM
[2024-01-24 13:46:24,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014235845.1_ASM1423584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014235845.1_ASM1423584v1_genomic.fna/checkm_input GCF_014235845.1_ASM1423584v1_genomic.fna/checkm_result
[2024-01-24 13:47:06,773] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:06,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,798] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:06,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:06,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014235845.1_ASM1423584v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:06,800] [INFO] Task started: Blastn
[2024-01-24 13:47:06,800] [INFO] Running command: blastn -query GCF_014235845.1_ASM1423584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg693e87ae-e2ad-457f-a00e-ef9e77ce0a61/dqc_reference/reference_markers_gtdb.fasta -out GCF_014235845.1_ASM1423584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:08,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:08,580] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:08,580] [INFO] Target genome list was writen to GCF_014235845.1_ASM1423584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:08,608] [INFO] Task started: fastANI
[2024-01-24 13:47:08,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg408dd169-9b34-46d9-8045-9d3a2c93e87c/GCF_014235845.1_ASM1423584v1_genomic.fna.gz --refList GCF_014235845.1_ASM1423584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014235845.1_ASM1423584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:23,517] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:23,533] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:23,534] [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_011290545.1	s__Monaibacterium sp011290545	96.729	1030	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	96.75	96.75	0.88	0.88	2	conclusive
GCF_900231835.1	s__Monaibacterium marinum	80.2984	587	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679265.1	s__MT2928 sp015679265	78.5896	432	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302495.1	s__Pontivivens insulae	78.2196	291	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521865.1	s__Roseivivax isoporae	77.998	208	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.5529	220	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	77.5423	186	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_005887635.2	s__Paroceanicella profunda	77.5065	251	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.4458	239	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_009789075.1	s__Pseudooceanicola pacificus	77.4442	204	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	77.3138	221	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	77.311	233	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011308835.1	s__Paracoccus xiamenensis	76.976	157	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	76.9469	187	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	76.9424	225	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	76.9195	236	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_000521785.1	s__Roseivivax halodurans	76.8853	174	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	76.8726	174	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_014201905.1	s__Amaricoccus macauensis	76.7915	140	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046725.1	s__DSPG01 sp011046725	76.553	163	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DSPG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,536] [INFO] GTDB search result was written to GCF_014235845.1_ASM1423584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:23,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:23,543] [INFO] DFAST_QC result json was written to GCF_014235845.1_ASM1423584v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:23,543] [INFO] DFAST_QC completed!
[2024-01-24 13:47:23,543] [INFO] Total running time: 0h1m37s