[2024-01-25 19:24:50,658] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:50,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:50,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference
[2024-01-25 19:24:51,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:51,818] [INFO] Task started: Prodigal
[2024-01-25 19:24:51,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgaee114d4-aed3-4026-bb45-88cacfe71d93/GCF_000409775.1_Han1.0_genomic.fna.gz | prodigal -d GCF_000409775.1_Han1.0_genomic.fna/cds.fna -a GCF_000409775.1_Han1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:25:06,481] [INFO] Task succeeded: Prodigal
[2024-01-25 19:25:06,482] [INFO] Task started: HMMsearch
[2024-01-25 19:25:06,482] [INFO] Running command: hmmsearch --tblout GCF_000409775.1_Han1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference/reference_markers.hmm GCF_000409775.1_Han1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:25:06,776] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:25:06,777] [INFO] Found 6/6 markers.
[2024-01-25 19:25:06,825] [INFO] Query marker FASTA was written to GCF_000409775.1_Han1.0_genomic.fna/markers.fasta
[2024-01-25 19:25:06,825] [INFO] Task started: Blastn
[2024-01-25 19:25:06,825] [INFO] Running command: blastn -query GCF_000409775.1_Han1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference/reference_markers.fasta -out GCF_000409775.1_Han1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:07,547] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:07,554] [INFO] Selected 21 target genomes.
[2024-01-25 19:25:07,555] [INFO] Target genome list was writen to GCF_000409775.1_Han1.0_genomic.fna/target_genomes.txt
[2024-01-25 19:25:07,606] [INFO] Task started: fastANI
[2024-01-25 19:25:07,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee114d4-aed3-4026-bb45-88cacfe71d93/GCF_000409775.1_Han1.0_genomic.fna.gz --refList GCF_000409775.1_Han1.0_genomic.fna/target_genomes.txt --output GCF_000409775.1_Han1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:26,193] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:26,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:26,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:26,206] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:26,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:26,207] [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
Halomonas anticariensis	strain=FP35	GCA_000409775.1	258591	258591	type	True	100.0	1677	1678	95	conclusive
Halomonas anticariensis	strain=DSM 16096	GCA_000428505.1	258591	258591	type	True	99.97	1627	1678	95	conclusive
Halomonas qijiaojingensis	strain=KCTC 22228	GCA_014651875.1	980347	980347	type	True	84.0587	1125	1678	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	79.9175	656	1678	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	79.8783	668	1678	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	79.6603	578	1678	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	79.5998	605	1678	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	79.5173	545	1678	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.4923	548	1678	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.3733	562	1678	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.3639	454	1678	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	79.337	545	1678	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.3309	469	1678	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	79.3084	542	1678	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	79.2589	489	1678	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	79.2395	507	1678	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	79.2049	533	1678	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.1914	456	1678	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	79.1623	462	1678	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.0953	523	1678	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.8625	441	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:26,208] [INFO] DFAST Taxonomy check result was written to GCF_000409775.1_Han1.0_genomic.fna/tc_result.tsv
[2024-01-25 19:25:26,209] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:26,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:26,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference/checkm_data
[2024-01-25 19:25:26,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:26,259] [INFO] Task started: CheckM
[2024-01-25 19:25:26,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000409775.1_Han1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000409775.1_Han1.0_genomic.fna/checkm_input GCF_000409775.1_Han1.0_genomic.fna/checkm_result
[2024-01-25 19:26:09,772] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:09,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:09,821] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:09,822] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:09,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000409775.1_Han1.0_genomic.fna/markers.fasta)
[2024-01-25 19:26:09,823] [INFO] Task started: Blastn
[2024-01-25 19:26:09,823] [INFO] Running command: blastn -query GCF_000409775.1_Han1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg59942df4-4196-411c-8649-9b809b370b26/dqc_reference/reference_markers_gtdb.fasta -out GCF_000409775.1_Han1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:10,877] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:10,882] [INFO] Selected 19 target genomes.
[2024-01-25 19:26:10,882] [INFO] Target genome list was writen to GCF_000409775.1_Han1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:10,891] [INFO] Task started: fastANI
[2024-01-25 19:26:10,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee114d4-aed3-4026-bb45-88cacfe71d93/GCF_000409775.1_Han1.0_genomic.fna.gz --refList GCF_000409775.1_Han1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000409775.1_Han1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:26:27,292] [INFO] Task succeeded: fastANI
[2024-01-25 19:26:27,303] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:26:27,303] [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_000409775.1	s__Halomonas_A anticariensis	100.0	1677	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014651875.1	s__Halomonas_A qijiaojingensis	84.0563	1124	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	79.9104	658	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010977575.1	s__Halomonas_B socia	79.6246	587	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	79.5437	579	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	79.4947	547	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	79.3536	455	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_003254665.1	s__Halomonas lactosivorans	79.3207	548	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	79.3043	542	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	79.2968	455	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	79.2588	489	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014840935.1	s__Halomonas_E sp014840935	79.2415	487	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	79.2136	532	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_014193375.1	s__Halomonas campaniensis	79.1791	460	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645095.1	s__Halomonas_F sp015645095	79.1019	509	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931605.1	s__Halomonas sp014931605	78.9886	499	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013009075.1	s__Halomonas_B sp013009075	78.8841	456	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	99.96	99.96	1.00	0.99	3	-
GCF_003182195.1	s__Halomonas sp003182195	78.8713	385	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_902500215.1	s__Halomonas sp902500215	78.8528	442	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:26:27,306] [INFO] GTDB search result was written to GCF_000409775.1_Han1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 19:26:27,307] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:26:27,311] [INFO] DFAST_QC result json was written to GCF_000409775.1_Han1.0_genomic.fna/dqc_result.json
[2024-01-25 19:26:27,311] [INFO] DFAST_QC completed!
[2024-01-25 19:26:27,311] [INFO] Total running time: 0h1m37s