[2023-06-30 20:51:02,080] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:51:02,082] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:51:02,082] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference
[2023-06-30 20:51:03,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:51:03,303] [INFO] Task started: Prodigal
[2023-06-30 20:51:03,303] [INFO] Running command: gunzip -c /var/lib/cwl/stgd482c780-3cd3-4e47-ab75-448607b5f720/GCA_016708905.1_ASM1670890v1_genomic.fna.gz | prodigal -d GCA_016708905.1_ASM1670890v1_genomic.fna/cds.fna -a GCA_016708905.1_ASM1670890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:51:19,292] [INFO] Task succeeded: Prodigal
[2023-06-30 20:51:19,292] [INFO] Task started: HMMsearch
[2023-06-30 20:51:19,293] [INFO] Running command: hmmsearch --tblout GCA_016708905.1_ASM1670890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference/reference_markers.hmm GCA_016708905.1_ASM1670890v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:51:19,585] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:51:19,587] [INFO] Found 6/6 markers.
[2023-06-30 20:51:19,627] [INFO] Query marker FASTA was written to GCA_016708905.1_ASM1670890v1_genomic.fna/markers.fasta
[2023-06-30 20:51:19,628] [INFO] Task started: Blastn
[2023-06-30 20:51:19,628] [INFO] Running command: blastn -query GCA_016708905.1_ASM1670890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference/reference_markers.fasta -out GCA_016708905.1_ASM1670890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:51:20,497] [INFO] Task succeeded: Blastn
[2023-06-30 20:51:20,501] [INFO] Selected 31 target genomes.
[2023-06-30 20:51:20,502] [INFO] Target genome list was writen to GCA_016708905.1_ASM1670890v1_genomic.fna/target_genomes.txt
[2023-06-30 20:51:20,504] [INFO] Task started: fastANI
[2023-06-30 20:51:20,504] [INFO] Running command: fastANI --query /var/lib/cwl/stgd482c780-3cd3-4e47-ab75-448607b5f720/GCA_016708905.1_ASM1670890v1_genomic.fna.gz --refList GCA_016708905.1_ASM1670890v1_genomic.fna/target_genomes.txt --output GCA_016708905.1_ASM1670890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:51:41,658] [INFO] Task succeeded: fastANI
[2023-06-30 20:51:41,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:51:41,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:51:41,693] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:51:41,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:51:41,693] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.2569	328	1665	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	78.2033	318	1665	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	77.9324	311	1665	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.8729	348	1665	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	77.8493	332	1665	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	77.8274	296	1665	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.8056	315	1665	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.7741	318	1665	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.7679	336	1665	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.7629	307	1665	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	77.7282	302	1665	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.7138	258	1665	95	below_threshold
Methyloversatilis thermotolerans	strain=3t	GCA_000372885.1	1346290	1346290	type	True	77.697	274	1665	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	77.6698	193	1665	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.6658	314	1665	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	77.6649	327	1665	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	77.5656	308	1665	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.5151	325	1665	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.4709	342	1665	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	77.4236	280	1665	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	77.416	293	1665	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.3798	281	1665	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.3554	282	1665	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	77.2848	257	1665	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	76.6524	179	1665	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	76.3757	212	1665	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	76.3239	162	1665	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.3184	246	1665	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.3104	228	1665	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	76.279	167	1665	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	76.229	210	1665	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:51:41,695] [INFO] DFAST Taxonomy check result was written to GCA_016708905.1_ASM1670890v1_genomic.fna/tc_result.tsv
[2023-06-30 20:51:41,696] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:51:41,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:51:41,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference/checkm_data
[2023-06-30 20:51:41,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:51:41,747] [INFO] Task started: CheckM
[2023-06-30 20:51:41,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708905.1_ASM1670890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708905.1_ASM1670890v1_genomic.fna/checkm_input GCA_016708905.1_ASM1670890v1_genomic.fna/checkm_result
[2023-06-30 20:52:30,787] [INFO] Task succeeded: CheckM
[2023-06-30 20:52:30,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:52:30,811] [INFO] ===== Completeness check finished =====
[2023-06-30 20:52:30,811] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:52:30,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708905.1_ASM1670890v1_genomic.fna/markers.fasta)
[2023-06-30 20:52:30,812] [INFO] Task started: Blastn
[2023-06-30 20:52:30,812] [INFO] Running command: blastn -query GCA_016708905.1_ASM1670890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5d44982-ec36-456d-8403-5f4d5de2c84c/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708905.1_ASM1670890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:52:32,283] [INFO] Task succeeded: Blastn
[2023-06-30 20:52:32,288] [INFO] Selected 19 target genomes.
[2023-06-30 20:52:32,289] [INFO] Target genome list was writen to GCA_016708905.1_ASM1670890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:52:32,292] [INFO] Task started: fastANI
[2023-06-30 20:52:32,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgd482c780-3cd3-4e47-ab75-448607b5f720/GCA_016708905.1_ASM1670890v1_genomic.fna.gz --refList GCA_016708905.1_ASM1670890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708905.1_ASM1670890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:52:46,564] [INFO] Task succeeded: fastANI
[2023-06-30 20:52:46,587] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:52:46,587] [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_016707455.1	s__JAEUNL01 sp016707455	99.6563	1508	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNL01	95.0	98.01	97.17	0.87	0.84	4	conclusive
GCA_016711925.1	s__JAEUNL01 sp016711925	83.4842	788	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791115.1	s__JAEUNL01 sp016791115	80.4013	567	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868295.1	s__Desulfobacillus sp016868295	78.3552	304	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339315.1	s__Desulfobacillus sp905339315	78.3213	216	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.66	96.66	0.91	0.89	3	-
GCA_016214145.1	s__Desulfobacillus sp016214145	78.2538	346	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791205.1	s__Desulfobacillus sp016791205	78.2368	276	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017347485.1	s__Desulfobacillus denitrificans	78.1931	349	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.90	98.32	0.92	0.90	5	-
GCA_008933825.1	s__Desulfobacillus sp008933825	78.1857	294	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCF_000310185.1	s__Thauera aminoaromatica	77.7999	314	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_018240785.1	s__Thauera sp018240785	77.7601	319	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	77.7542	340	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	77.5075	237	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_000310145.2	s__Thauera sp000310145	77.479	267	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.71	98.54	0.88	0.86	4	-
GCF_001274695.1	s__Aromatoleum sp001274695	77.408	275	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	77.1763	224	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241665.1	s__Zoogloea sp018241665	77.1695	287	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911025.1	s__Azoarcus sp012911025	77.1231	290	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904605.1	s__CAIYYX01 sp903904605	76.9144	203	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAIYYX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:52:46,589] [INFO] GTDB search result was written to GCA_016708905.1_ASM1670890v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:52:46,590] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:52:46,595] [INFO] DFAST_QC result json was written to GCA_016708905.1_ASM1670890v1_genomic.fna/dqc_result.json
[2023-06-30 20:52:46,595] [INFO] DFAST_QC completed!
[2023-06-30 20:52:46,595] [INFO] Total running time: 0h1m45s