[2023-07-01 00:36:16,291] [INFO] DFAST_QC pipeline started.
[2023-07-01 00:36:16,293] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 00:36:16,293] [INFO] DQC Reference Directory: /var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference
[2023-07-01 00:36:18,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 00:36:18,595] [INFO] Task started: Prodigal
[2023-07-01 00:36:18,596] [INFO] Running command: gunzip -c /var/lib/cwl/stgadbbbdb0-afc7-4f79-b460-c4b52bb5294f/GCA_025459035.1_ASM2545903v1_genomic.fna.gz | prodigal -d GCA_025459035.1_ASM2545903v1_genomic.fna/cds.fna -a GCA_025459035.1_ASM2545903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 00:36:25,253] [INFO] Task succeeded: Prodigal
[2023-07-01 00:36:25,254] [INFO] Task started: HMMsearch
[2023-07-01 00:36:25,254] [INFO] Running command: hmmsearch --tblout GCA_025459035.1_ASM2545903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference/reference_markers.hmm GCA_025459035.1_ASM2545903v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 00:36:25,483] [INFO] Task succeeded: HMMsearch
[2023-07-01 00:36:25,484] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgadbbbdb0-afc7-4f79-b460-c4b52bb5294f/GCA_025459035.1_ASM2545903v1_genomic.fna.gz]
[2023-07-01 00:36:25,511] [INFO] Query marker FASTA was written to GCA_025459035.1_ASM2545903v1_genomic.fna/markers.fasta
[2023-07-01 00:36:25,511] [INFO] Task started: Blastn
[2023-07-01 00:36:25,511] [INFO] Running command: blastn -query GCA_025459035.1_ASM2545903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference/reference_markers.fasta -out GCA_025459035.1_ASM2545903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:36:26,389] [INFO] Task succeeded: Blastn
[2023-07-01 00:36:26,394] [INFO] Selected 19 target genomes.
[2023-07-01 00:36:26,395] [INFO] Target genome list was writen to GCA_025459035.1_ASM2545903v1_genomic.fna/target_genomes.txt
[2023-07-01 00:36:26,397] [INFO] Task started: fastANI
[2023-07-01 00:36:26,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgadbbbdb0-afc7-4f79-b460-c4b52bb5294f/GCA_025459035.1_ASM2545903v1_genomic.fna.gz --refList GCA_025459035.1_ASM2545903v1_genomic.fna/target_genomes.txt --output GCA_025459035.1_ASM2545903v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 00:36:40,711] [INFO] Task succeeded: fastANI
[2023-07-01 00:36:40,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 00:36:40,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 00:36:40,730] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 00:36:40,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 00:36:40,731] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.2117	195	734	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.09	189	734	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.0587	189	734	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.0367	178	734	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.0224	176	734	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	76.9436	186	734	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.8783	202	734	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	76.8281	172	734	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.7353	216	734	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.6415	208	734	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	76.6264	205	734	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.6128	218	734	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	76.4722	130	734	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	76.3987	174	734	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	76.3721	180	734	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	76.0835	217	734	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	76.0827	148	734	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	75.9852	176	734	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	75.905	173	734	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 00:36:40,733] [INFO] DFAST Taxonomy check result was written to GCA_025459035.1_ASM2545903v1_genomic.fna/tc_result.tsv
[2023-07-01 00:36:40,733] [INFO] ===== Taxonomy check completed =====
[2023-07-01 00:36:40,733] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 00:36:40,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference/checkm_data
[2023-07-01 00:36:40,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 00:36:40,767] [INFO] Task started: CheckM
[2023-07-01 00:36:40,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025459035.1_ASM2545903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025459035.1_ASM2545903v1_genomic.fna/checkm_input GCA_025459035.1_ASM2545903v1_genomic.fna/checkm_result
[2023-07-01 00:37:17,834] [INFO] Task succeeded: CheckM
[2023-07-01 00:37:17,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 00:37:17,859] [INFO] ===== Completeness check finished =====
[2023-07-01 00:37:17,859] [INFO] ===== Start GTDB Search =====
[2023-07-01 00:37:17,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025459035.1_ASM2545903v1_genomic.fna/markers.fasta)
[2023-07-01 00:37:17,860] [INFO] Task started: Blastn
[2023-07-01 00:37:17,860] [INFO] Running command: blastn -query GCA_025459035.1_ASM2545903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f71a34-cd39-4a51-813f-781eb6a3d795/dqc_reference/reference_markers_gtdb.fasta -out GCA_025459035.1_ASM2545903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:37:19,404] [INFO] Task succeeded: Blastn
[2023-07-01 00:37:19,408] [INFO] Selected 22 target genomes.
[2023-07-01 00:37:19,409] [INFO] Target genome list was writen to GCA_025459035.1_ASM2545903v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 00:37:19,416] [INFO] Task started: fastANI
[2023-07-01 00:37:19,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgadbbbdb0-afc7-4f79-b460-c4b52bb5294f/GCA_025459035.1_ASM2545903v1_genomic.fna.gz --refList GCA_025459035.1_ASM2545903v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025459035.1_ASM2545903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 00:37:36,544] [INFO] Task succeeded: fastANI
[2023-07-01 00:37:36,577] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 00:37:36,578] [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_001464895.1	s__Ga0077526 sp001464895	78.4962	293	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464765.1	s__Ga0077526 sp001464765	77.7826	303	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125475.1	s__Ga0077526 sp016125475	77.505	245	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933825.1	s__Desulfobacillus sp008933825	77.3964	144	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCA_016716425.1	s__VBCG01 sp016716425	77.2519	278	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912485.1	s__CAIWHR01 sp903912485	77.2213	227	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	99.88	99.81	0.92	0.91	3	-
GCA_016704895.1	s__VBCG01 sp016704895	77.2058	269	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	96.62	96.45	0.90	0.90	3	-
GCA_001724855.1	s__SCN-69-89 sp001724855	77.1899	234	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791205.1	s__Desulfobacillus sp016791205	77.1274	142	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716275.1	s__JADJWR01 sp016716275	77.1237	218	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339295.1	s__VBCG01 sp905339295	77.0443	270	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909415.1	s__CAIVVS01 sp903909415	76.9257	179	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAIVVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	76.9046	202	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019137045.1	s__JAGVSZ01 sp019137045	76.8644	236	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JAGVSZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	76.8179	224	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725505.1	s__Rubrivivax sp001725505	76.712	236	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790695.1	s__JAEUOS01 sp016790695	76.6626	269	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789955.1	s__Rubrivivax sp016789955	76.4135	245	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078705.1	s__Bordetella_B ansorpii_A	76.2182	181	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223165.1	s__Rubrivivax sp016223165	76.2008	277	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078315.1	s__Bordetella_B ansorpii	76.1568	177	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004209755.1	s__Pseudoduganella lutea	75.9132	172	734	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 00:37:36,580] [INFO] GTDB search result was written to GCA_025459035.1_ASM2545903v1_genomic.fna/result_gtdb.tsv
[2023-07-01 00:37:36,581] [INFO] ===== GTDB Search completed =====
[2023-07-01 00:37:36,586] [INFO] DFAST_QC result json was written to GCA_025459035.1_ASM2545903v1_genomic.fna/dqc_result.json
[2023-07-01 00:37:36,586] [INFO] DFAST_QC completed!
[2023-07-01 00:37:36,586] [INFO] Total running time: 0h1m20s