[2024-01-24 15:10:21,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:21,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:21,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference
[2024-01-24 15:10:23,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:23,844] [INFO] Task started: Prodigal
[2024-01-24 15:10:23,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg793ee9a5-8256-46c9-9c14-91d04a3f3aed/GCF_004323635.1_ASM432363v1_genomic.fna.gz | prodigal -d GCF_004323635.1_ASM432363v1_genomic.fna/cds.fna -a GCF_004323635.1_ASM432363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:38,808] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:38,809] [INFO] Task started: HMMsearch
[2024-01-24 15:10:38,809] [INFO] Running command: hmmsearch --tblout GCF_004323635.1_ASM432363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference/reference_markers.hmm GCF_004323635.1_ASM432363v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:39,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:39,084] [INFO] Found 6/6 markers.
[2024-01-24 15:10:39,126] [INFO] Query marker FASTA was written to GCF_004323635.1_ASM432363v1_genomic.fna/markers.fasta
[2024-01-24 15:10:39,127] [INFO] Task started: Blastn
[2024-01-24 15:10:39,127] [INFO] Running command: blastn -query GCF_004323635.1_ASM432363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference/reference_markers.fasta -out GCF_004323635.1_ASM432363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:39,965] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:39,968] [INFO] Selected 29 target genomes.
[2024-01-24 15:10:39,969] [INFO] Target genome list was writen to GCF_004323635.1_ASM432363v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:39,979] [INFO] Task started: fastANI
[2024-01-24 15:10:39,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg793ee9a5-8256-46c9-9c14-91d04a3f3aed/GCF_004323635.1_ASM432363v1_genomic.fna.gz --refList GCF_004323635.1_ASM432363v1_genomic.fna/target_genomes.txt --output GCF_004323635.1_ASM432363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:03,954] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:03,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:03,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:03,976] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:03,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:03,976] [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
Lichenihabitans psoromatis	strain=PAMC 29148	GCA_004323635.1	2528642	2528642	type	True	100.0	1609	1610	95	conclusive
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	77.2411	383	1610	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	77.2236	354	1610	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	77.0012	184	1610	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_004135935.1	569860	569860	type	True	76.9393	156	1610	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_003387225.1	569860	569860	type	True	76.9074	152	1610	95	below_threshold
Methyloferula stellata	strain=AR4T	GCA_000385335.1	876270	876270	type	True	76.8199	157	1610	95	below_threshold
Methylocapsa palsarum	strain=NE2	GCA_900114285.1	1612308	1612308	type	True	76.809	139	1610	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	76.7485	176	1610	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	76.6788	184	1610	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	76.657	135	1610	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.6301	218	1610	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.5856	214	1610	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	76.5609	140	1610	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	76.5153	179	1610	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	76.4767	158	1610	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.4538	226	1610	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	76.3631	155	1610	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	76.3548	178	1610	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	76.3497	169	1610	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	76.3155	166	1610	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3008	255	1610	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.2798	241	1610	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	76.2435	144	1610	95	below_threshold
Methylobacterium bullatum	strain=LMG 24788	GCA_014845095.1	570505	570505	type	True	76.2053	164	1610	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.1789	175	1610	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	76.1168	234	1610	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.8917	197	1610	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.6048	161	1610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:03,978] [INFO] DFAST Taxonomy check result was written to GCF_004323635.1_ASM432363v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:03,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:03,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:03,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference/checkm_data
[2024-01-24 15:11:03,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:04,027] [INFO] Task started: CheckM
[2024-01-24 15:11:04,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004323635.1_ASM432363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004323635.1_ASM432363v1_genomic.fna/checkm_input GCF_004323635.1_ASM432363v1_genomic.fna/checkm_result
[2024-01-24 15:11:50,360] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:50,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:50,384] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:50,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:50,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004323635.1_ASM432363v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:50,385] [INFO] Task started: Blastn
[2024-01-24 15:11:50,385] [INFO] Running command: blastn -query GCF_004323635.1_ASM432363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4eded939-a7bc-44d2-8fa2-ba270f21bfaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004323635.1_ASM432363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:51,923] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:51,928] [INFO] Selected 25 target genomes.
[2024-01-24 15:11:51,928] [INFO] Target genome list was writen to GCF_004323635.1_ASM432363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:51,945] [INFO] Task started: fastANI
[2024-01-24 15:11:51,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg793ee9a5-8256-46c9-9c14-91d04a3f3aed/GCF_004323635.1_ASM432363v1_genomic.fna.gz --refList GCF_004323635.1_ASM432363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004323635.1_ASM432363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:12,316] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:12,336] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:12,337] [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_004323635.1	s__Lichenihabitans psoromatis	100.0	1608	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	97.95	97.95	0.93	0.93	2	conclusive
GCF_004137085.1	s__Lichenihabitans ramalinae	77.2257	385	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137685.1	s__Lichenihabitans minor	77.2228	354	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021745.1	s__Methylocella silvestris	77.0623	185	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901905185.1	s__Methylocella tundrae	76.8093	146	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	97.31	97.31	0.88	0.88	2	-
GCF_900114285.1	s__Methylocella palsarum	76.809	139	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385335.1	s__Methyloferula stellata	76.8045	158	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746085.1	s__Methylocella aurea	76.7956	133	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709455.1	s__Methylosinus sp015709455	76.7927	157	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891535.1	s__Methylocella silvestris_A	76.7535	179	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426225.1	s__Bosea sp001426225	76.7427	187	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104955.1	s__28-YEA-48 sp900104955	76.7414	167	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	76.7044	175	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188155.2	s__Methylocystis sp000188155	76.6942	167	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916165.1	s__28-YEA-48 sp903916165	76.5743	108	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	96.66	95.33	0.74	0.69	4	-
GCF_003173735.1	s__Methylobacterium radiodurans	76.5697	196	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745215.1	s__Methylosinus sp000745215	76.4991	180	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	76.4725	191	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	76.4721	240	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351345.1	s__Bosea caraganae	76.4529	226	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003347665.1	s__Microvirga calopogonii	76.4118	172	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003113265.1	s__Methylosinus sporium	76.3155	166	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	98.07	97.36	0.91	0.86	5	-
GCA_013377085.1	s__Rhodoplanes sp013377085	76.2651	204	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918155.1	s__28-YEA-48 sp903918155	76.1552	100	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884435.1	s__28-YEA-48 sp903884435	75.6614	121	1610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:12,338] [INFO] GTDB search result was written to GCF_004323635.1_ASM432363v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:12,339] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:12,345] [INFO] DFAST_QC result json was written to GCF_004323635.1_ASM432363v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:12,345] [INFO] DFAST_QC completed!
[2024-01-24 15:12:12,345] [INFO] Total running time: 0h1m51s