[2024-01-24 11:43:52,850] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,852] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,852] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference
[2024-01-24 11:43:54,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,132] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg865559fc-9029-46a1-a4cd-5c16bb02899e/GCF_014750705.1_ASM1475070v1_genomic.fna.gz | prodigal -d GCF_014750705.1_ASM1475070v1_genomic.fna/cds.fna -a GCF_014750705.1_ASM1475070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:06,466] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:06,467] [INFO] Task started: HMMsearch
[2024-01-24 11:44:06,467] [INFO] Running command: hmmsearch --tblout GCF_014750705.1_ASM1475070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference/reference_markers.hmm GCF_014750705.1_ASM1475070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:06,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:06,717] [INFO] Found 6/6 markers.
[2024-01-24 11:44:06,770] [INFO] Query marker FASTA was written to GCF_014750705.1_ASM1475070v1_genomic.fna/markers.fasta
[2024-01-24 11:44:06,771] [INFO] Task started: Blastn
[2024-01-24 11:44:06,771] [INFO] Running command: blastn -query GCF_014750705.1_ASM1475070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference/reference_markers.fasta -out GCF_014750705.1_ASM1475070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:07,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:07,665] [INFO] Selected 28 target genomes.
[2024-01-24 11:44:07,665] [INFO] Target genome list was writen to GCF_014750705.1_ASM1475070v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:07,675] [INFO] Task started: fastANI
[2024-01-24 11:44:07,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg865559fc-9029-46a1-a4cd-5c16bb02899e/GCF_014750705.1_ASM1475070v1_genomic.fna.gz --refList GCF_014750705.1_ASM1475070v1_genomic.fna/target_genomes.txt --output GCF_014750705.1_ASM1475070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:30,247] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:30,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:30,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:30,267] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:30,268] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:30,268] [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
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	84.4302	868	1204	95	below_threshold
Arboricoccus pini	strain=B29T1	GCA_900187945.1	1963835	1963835	type	True	77.0947	132	1204	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.8956	316	1204	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.8891	319	1204	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.8681	200	1204	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.839	282	1204	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.8378	250	1204	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.7846	171	1204	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7683	288	1204	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	76.7475	140	1204	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.715	182	1204	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.6922	142	1204	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.619	138	1204	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.5923	189	1204	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.5895	152	1204	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.5466	147	1204	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	76.5412	164	1204	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.4742	267	1204	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.4565	178	1204	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	76.397	207	1204	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.3968	201	1204	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	76.3536	167	1204	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	76.343	113	1204	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	76.3388	112	1204	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.299	216	1204	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.294	176	1204	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.2841	236	1204	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	76.0601	108	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:30,270] [INFO] DFAST Taxonomy check result was written to GCF_014750705.1_ASM1475070v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:30,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:30,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:30,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference/checkm_data
[2024-01-24 11:44:30,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:30,319] [INFO] Task started: CheckM
[2024-01-24 11:44:30,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014750705.1_ASM1475070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014750705.1_ASM1475070v1_genomic.fna/checkm_input GCF_014750705.1_ASM1475070v1_genomic.fna/checkm_result
[2024-01-24 11:45:08,061] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:08,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:08,078] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:08,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:08,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014750705.1_ASM1475070v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:08,078] [INFO] Task started: Blastn
[2024-01-24 11:45:08,078] [INFO] Running command: blastn -query GCF_014750705.1_ASM1475070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1d21fa4-1226-4625-88f3-2be0ed28a302/dqc_reference/reference_markers_gtdb.fasta -out GCF_014750705.1_ASM1475070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:09,687] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:09,690] [INFO] Selected 26 target genomes.
[2024-01-24 11:45:09,691] [INFO] Target genome list was writen to GCF_014750705.1_ASM1475070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:09,733] [INFO] Task started: fastANI
[2024-01-24 11:45:09,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg865559fc-9029-46a1-a4cd-5c16bb02899e/GCF_014750705.1_ASM1475070v1_genomic.fna.gz --refList GCF_014750705.1_ASM1475070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014750705.1_ASM1475070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:30,167] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:30,187] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:45:30,187] [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_000427665.1	s__Geminicoccus roseus	84.4315	867	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Geminicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826935.1	s__CADEGR01 sp902826935	77.6285	303	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCA_007131045.1	s__SLRI01 sp007131045	77.5391	196	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390475.1	s__SLRI01 sp011390475	77.4232	208	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187945.1	s__Arboricoccus pini	77.0947	132	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Arboricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.8371	202	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003130795.1	s__Azospirillum thermophilum	76.8357	284	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	76.788	190	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.7713	173	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCA_015490605.1	s__HRBIN39 sp015490605	76.731	115	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__HRBIN39	95.0	97.05	97.05	0.84	0.84	2	-
GCF_003116015.1	s__Azospirillum sp003116015	76.7016	298	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	76.5958	194	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308495.1	s__Afipia sp017308495	76.5353	128	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.5321	193	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	76.5286	165	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	76.4602	167	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	76.4598	269	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	76.4261	213	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	76.4069	200	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312425.1	s__Reyranella massiliensis	76.3769	167	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429045.1	s__Salinarimonas rosea	76.3046	214	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	76.2803	150	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001939945.1	s__Aerophototrophica crusticola	76.2735	201	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Aerophototrophica	95.0	99.94	99.94	0.97	0.97	2	-
GCA_019235415.1	s__Reyranella sp019235415	76.2726	186	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.35	99.35	0.86	0.86	2	-
GCA_016869645.1	s__SHVW01 sp016869645	76.2031	188	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.0595	141	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:30,189] [INFO] GTDB search result was written to GCF_014750705.1_ASM1475070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:30,190] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:30,195] [INFO] DFAST_QC result json was written to GCF_014750705.1_ASM1475070v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:30,196] [INFO] DFAST_QC completed!
[2024-01-24 11:45:30,196] [INFO] Total running time: 0h1m37s