[2023-06-07 19:05:03,160] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:05:03,162] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:05:03,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference
[2023-06-07 19:05:04,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:05:04,460] [INFO] Task started: Prodigal
[2023-06-07 19:05:04,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg72d18c13-38d9-4cda-ac66-9d6483a64f75/GCA_945867705.1_MiE-16apr19-242_genomic.fna.gz | prodigal -d GCA_945867705.1_MiE-16apr19-242_genomic.fna/cds.fna -a GCA_945867705.1_MiE-16apr19-242_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:05:15,054] [INFO] Task succeeded: Prodigal
[2023-06-07 19:05:15,055] [INFO] Task started: HMMsearch
[2023-06-07 19:05:15,055] [INFO] Running command: hmmsearch --tblout GCA_945867705.1_MiE-16apr19-242_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference/reference_markers.hmm GCA_945867705.1_MiE-16apr19-242_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:05:15,305] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:05:15,306] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg72d18c13-38d9-4cda-ac66-9d6483a64f75/GCA_945867705.1_MiE-16apr19-242_genomic.fna.gz]
[2023-06-07 19:05:15,338] [INFO] Query marker FASTA was written to GCA_945867705.1_MiE-16apr19-242_genomic.fna/markers.fasta
[2023-06-07 19:05:15,339] [INFO] Task started: Blastn
[2023-06-07 19:05:15,339] [INFO] Running command: blastn -query GCA_945867705.1_MiE-16apr19-242_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference/reference_markers.fasta -out GCA_945867705.1_MiE-16apr19-242_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:15,904] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:15,908] [INFO] Selected 24 target genomes.
[2023-06-07 19:05:15,908] [INFO] Target genome list was writen to GCA_945867705.1_MiE-16apr19-242_genomic.fna/target_genomes.txt
[2023-06-07 19:05:15,912] [INFO] Task started: fastANI
[2023-06-07 19:05:15,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg72d18c13-38d9-4cda-ac66-9d6483a64f75/GCA_945867705.1_MiE-16apr19-242_genomic.fna.gz --refList GCA_945867705.1_MiE-16apr19-242_genomic.fna/target_genomes.txt --output GCA_945867705.1_MiE-16apr19-242_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:05:35,329] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:35,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:05:35,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:05:35,349] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:05:35,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 19:05:35,350] [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
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	79.0632	319	907	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.6495	269	907	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.6434	288	907	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	78.6132	315	907	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.4899	315	907	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.4873	334	907	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.4291	335	907	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	78.367	318	907	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	78.3643	269	907	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	78.3528	316	907	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	78.2956	316	907	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.1983	282	907	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	78.1187	245	907	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	78.076	304	907	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	78.0117	262	907	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	77.9023	261	907	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	77.8652	236	907	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	77.7978	244	907	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	77.6957	266	907	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	77.6125	212	907	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	77.5897	213	907	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	77.5641	218	907	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.4415	224	907	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	77.422	252	907	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 19:05:35,352] [INFO] DFAST Taxonomy check result was written to GCA_945867705.1_MiE-16apr19-242_genomic.fna/tc_result.tsv
[2023-06-07 19:05:35,353] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:05:35,353] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:05:35,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference/checkm_data
[2023-06-07 19:05:35,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:05:35,393] [INFO] Task started: CheckM
[2023-06-07 19:05:35,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945867705.1_MiE-16apr19-242_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945867705.1_MiE-16apr19-242_genomic.fna/checkm_input GCA_945867705.1_MiE-16apr19-242_genomic.fna/checkm_result
[2023-06-07 19:06:10,488] [INFO] Task succeeded: CheckM
[2023-06-07 19:06:10,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:06:10,511] [INFO] ===== Completeness check finished =====
[2023-06-07 19:06:10,511] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:06:10,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945867705.1_MiE-16apr19-242_genomic.fna/markers.fasta)
[2023-06-07 19:06:10,512] [INFO] Task started: Blastn
[2023-06-07 19:06:10,512] [INFO] Running command: blastn -query GCA_945867705.1_MiE-16apr19-242_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29cd0aa-16ff-4bbe-9f2d-487ac1e5c4ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_945867705.1_MiE-16apr19-242_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:06:11,224] [INFO] Task succeeded: Blastn
[2023-06-07 19:06:11,229] [INFO] Selected 25 target genomes.
[2023-06-07 19:06:11,230] [INFO] Target genome list was writen to GCA_945867705.1_MiE-16apr19-242_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:06:11,243] [INFO] Task started: fastANI
[2023-06-07 19:06:11,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg72d18c13-38d9-4cda-ac66-9d6483a64f75/GCA_945867705.1_MiE-16apr19-242_genomic.fna.gz --refList GCA_945867705.1_MiE-16apr19-242_genomic.fna/target_genomes_gtdb.txt --output GCA_945867705.1_MiE-16apr19-242_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:06:28,724] [INFO] Task succeeded: fastANI
[2023-06-07 19:06:28,756] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 19:06:28,757] [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
GCA_005503335.1	s__SCMQ01 sp005503335	79.2041	328	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002278925.1	s__Polaromonas sp002278925	79.0847	293	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	99.99	99.98	0.99	0.99	5	-
GCF_001598235.1	s__Polaromonas jejuensis	79.048	321	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	78.8324	295	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001432305.1	s__Hylemonella sp001432305	78.8061	279	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063435.1	s__Limnohabitans_A sp003063435	78.7813	306	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000195.1	s__Polaromonas sp016000195	78.7667	250	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	98.70	98.70	0.94	0.94	2	-
GCF_003063665.1	s__Limnohabitans_A sp003063665	78.7659	306	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.02	95.55	0.82	0.79	4	-
GCF_002379095.1	s__Polaromonas sp002379095	78.717	344	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	78.6902	261	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013865.1	s__Polaromonas sp000013865	78.6561	313	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797315.1	s__Hylemonella sp001797315	78.5799	266	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003063505.1	s__Limnohabitans_A sp003063505	78.5734	267	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652235.1	s__Pseudorhodoferax aquiterrae	78.49	315	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	78.4753	335	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_000175235.1	s__Acidovorax delafieldii_B	78.4615	239	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916355.1	s__Limnohabitans_A sp903916355	78.3033	240	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.87	99.87	0.93	0.93	2	-
GCA_016868205.1	s__Polaromonas sp016868205	78.2246	241	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100305.1	s__Acidovorax_A citrulli	78.1187	245	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_002001015.1	s__Polaromonas sp002001015	78.1012	266	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591345.1	s__Variovorax boronicumulans	78.0641	305	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	97.15	97.07	0.92	0.90	8	-
GCA_903886275.1	s__Rhodoferax sp903886275	78.0121	275	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCF_000176855.2	s__Acidovorax_A avenae	78.0103	262	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCF_003952185.1	s__Variovorax sp003952185	77.8888	272	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.99	99.98	0.99	0.99	3	-
GCF_003063415.1	s__Limnohabitans_A sp003063415	77.6961	248	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:06:28,759] [INFO] GTDB search result was written to GCA_945867705.1_MiE-16apr19-242_genomic.fna/result_gtdb.tsv
[2023-06-07 19:06:28,760] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:06:28,765] [INFO] DFAST_QC result json was written to GCA_945867705.1_MiE-16apr19-242_genomic.fna/dqc_result.json
[2023-06-07 19:06:28,766] [INFO] DFAST_QC completed!
[2023-06-07 19:06:28,766] [INFO] Total running time: 0h1m26s