[2024-01-24 12:14:10,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,032] [INFO] DQC Reference Directory: /var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference
[2024-01-24 12:14:11,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,400] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,400] [INFO] Running command: gunzip -c /var/lib/cwl/stgabfa87dc-7235-4f02-9719-9081a11f62f9/GCF_024170285.1_ASM2417028v1_genomic.fna.gz | prodigal -d GCF_024170285.1_ASM2417028v1_genomic.fna/cds.fna -a GCF_024170285.1_ASM2417028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:26,277] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:26,278] [INFO] Task started: HMMsearch
[2024-01-24 12:14:26,278] [INFO] Running command: hmmsearch --tblout GCF_024170285.1_ASM2417028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference/reference_markers.hmm GCF_024170285.1_ASM2417028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:26,616] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:26,618] [INFO] Found 6/6 markers.
[2024-01-24 12:14:26,668] [INFO] Query marker FASTA was written to GCF_024170285.1_ASM2417028v1_genomic.fna/markers.fasta
[2024-01-24 12:14:26,668] [INFO] Task started: Blastn
[2024-01-24 12:14:26,669] [INFO] Running command: blastn -query GCF_024170285.1_ASM2417028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference/reference_markers.fasta -out GCF_024170285.1_ASM2417028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:27,641] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:27,645] [INFO] Selected 30 target genomes.
[2024-01-24 12:14:27,645] [INFO] Target genome list was writen to GCF_024170285.1_ASM2417028v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:27,660] [INFO] Task started: fastANI
[2024-01-24 12:14:27,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgabfa87dc-7235-4f02-9719-9081a11f62f9/GCF_024170285.1_ASM2417028v1_genomic.fna.gz --refList GCF_024170285.1_ASM2417028v1_genomic.fna/target_genomes.txt --output GCF_024170285.1_ASM2417028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:50,419] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:50,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:50,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:50,440] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:50,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:50,440] [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
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	100.0	1508	1508	95	conclusive
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.9229	287	1508	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	77.6419	214	1508	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	77.0446	175	1508	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.9369	167	1508	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	76.7942	114	1508	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.739	145	1508	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.7078	97	1508	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.6405	110	1508	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	76.6281	117	1508	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.5671	127	1508	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.4435	120	1508	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.3634	111	1508	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3168	100	1508	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.2706	91	1508	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.2271	96	1508	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.1929	131	1508	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.1615	112	1508	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.1485	113	1508	95	below_threshold
Fluviicoccus keumensis	strain=DSM 105135	GCA_004217445.1	1435465	1435465	type	True	75.8819	52	1508	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	75.8618	102	1508	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	75.8189	87	1508	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.7343	83	1508	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.6977	79	1508	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	74.765	68	1508	95	below_threshold
Streptomyces lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	74.7572	52	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:50,442] [INFO] DFAST Taxonomy check result was written to GCF_024170285.1_ASM2417028v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:50,443] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:50,443] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:50,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference/checkm_data
[2024-01-24 12:14:50,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:50,495] [INFO] Task started: CheckM
[2024-01-24 12:14:50,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024170285.1_ASM2417028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024170285.1_ASM2417028v1_genomic.fna/checkm_input GCF_024170285.1_ASM2417028v1_genomic.fna/checkm_result
[2024-01-24 12:15:34,862] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:34,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,887] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:34,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:34,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024170285.1_ASM2417028v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:34,888] [INFO] Task started: Blastn
[2024-01-24 12:15:34,888] [INFO] Running command: blastn -query GCF_024170285.1_ASM2417028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18be6b9-e53e-49f5-bb09-7478b59db7ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_024170285.1_ASM2417028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:36,521] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:36,526] [INFO] Selected 33 target genomes.
[2024-01-24 12:15:36,526] [INFO] Target genome list was writen to GCF_024170285.1_ASM2417028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:36,553] [INFO] Task started: fastANI
[2024-01-24 12:15:36,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgabfa87dc-7235-4f02-9719-9081a11f62f9/GCF_024170285.1_ASM2417028v1_genomic.fna.gz --refList GCF_024170285.1_ASM2417028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024170285.1_ASM2417028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:54,203] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:54,225] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:54,225] [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_003564975.1	s__SLLM01 sp003564975	98.5886	612	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SLLM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012044895.1	s__Aquisalimonas sp012044895	78.3328	305	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134055.1	s__SLLM01 sp007134055	78.131	360	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SLLM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110585.1	s__Aquisalimonas asiatica	77.935	286	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127625.1	s__Aquisalimonas sp007127625	77.5626	200	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	98.40	98.40	0.79	0.79	2	-
GCA_007117515.1	s__SKGQ01 sp007117515	77.5375	159	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SKGQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125985.1	s__LSCE01 sp007125985	77.4855	234	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__LSCE01	95.0	99.32	99.28	0.92	0.89	3	-
GCF_009295635.1	s__S0819 sp009295635	77.4687	195	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003565775.1	s__SKGQ01 sp003565775	77.4183	224	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SKGQ01	95.0	99.57	99.57	0.95	0.95	2	-
GCA_007126095.1	s__Aquisalimonas sp007126095	77.3905	263	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	99.75	99.73	0.94	0.94	3	-
GCA_007130525.1	s__SLSJ01 sp007130525	77.3213	160	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SLSJ01	95.0	99.73	99.72	0.86	0.79	3	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.061	125	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	77.0446	175	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089885.1	s__XN24 sp011089885	76.6849	93	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	76.6447	90	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.4435	120	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	76.2889	95	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428405.1	s__Frateuria_A sp001428405	76.2253	102	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	76.1861	116	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	76.1499	113	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.1111	122	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	76.0954	95	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391525.1	s__Competibacter_A sp002391525	75.9763	74	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.79	99.79	0.93	0.93	2	-
GCF_003789045.1	s__Marinobacter_A sp003789045	75.9263	84	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCA_001899775.1	s__Thiobacillus sp001899775	75.915	52	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	75.6919	79	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:54,227] [INFO] GTDB search result was written to GCF_024170285.1_ASM2417028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:54,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:54,232] [INFO] DFAST_QC result json was written to GCF_024170285.1_ASM2417028v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:54,232] [INFO] DFAST_QC completed!
[2024-01-24 12:15:54,232] [INFO] Total running time: 0h1m44s