[2024-01-24 13:45:41,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,741] [INFO] DQC Reference Directory: /var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference
[2024-01-24 13:45:42,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,934] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ee14b6d-95a6-4041-9d65-ac60c10e6aab/GCF_021412585.1_ASM2141258v1_genomic.fna.gz | prodigal -d GCF_021412585.1_ASM2141258v1_genomic.fna/cds.fna -a GCF_021412585.1_ASM2141258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:57,439] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:57,440] [INFO] Task started: HMMsearch
[2024-01-24 13:45:57,440] [INFO] Running command: hmmsearch --tblout GCF_021412585.1_ASM2141258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference/reference_markers.hmm GCF_021412585.1_ASM2141258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:57,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:57,740] [INFO] Found 6/6 markers.
[2024-01-24 13:45:57,791] [INFO] Query marker FASTA was written to GCF_021412585.1_ASM2141258v1_genomic.fna/markers.fasta
[2024-01-24 13:45:57,792] [INFO] Task started: Blastn
[2024-01-24 13:45:57,792] [INFO] Running command: blastn -query GCF_021412585.1_ASM2141258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference/reference_markers.fasta -out GCF_021412585.1_ASM2141258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:58,784] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:58,787] [INFO] Selected 16 target genomes.
[2024-01-24 13:45:58,788] [INFO] Target genome list was writen to GCF_021412585.1_ASM2141258v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:58,807] [INFO] Task started: fastANI
[2024-01-24 13:45:58,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee14b6d-95a6-4041-9d65-ac60c10e6aab/GCF_021412585.1_ASM2141258v1_genomic.fna.gz --refList GCF_021412585.1_ASM2141258v1_genomic.fna/target_genomes.txt --output GCF_021412585.1_ASM2141258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:16,229] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:16,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:16,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:16,248] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:16,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:16,249] [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 alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	100.0	1597	1601	95	conclusive
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	92.5478	1218	1601	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	83.9855	1001	1601	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	83.9523	977	1601	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.9048	944	1601	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	83.8263	1003	1601	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.7035	1010	1601	95	below_threshold
Halomonas endophytica	strain=MC28	GCA_002879615.1	2033802	2033802	type	True	83.5605	935	1601	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	83.5133	1082	1601	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	83.3863	1057	1601	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	83.1283	1026	1601	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	83.0849	880	1601	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	82.9035	963	1601	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	82.8138	955	1601	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	82.7276	955	1601	95	below_threshold
Halomonas pellis	strain=L5	GCA_008297955.1	2606936	2606936	type	True	81.9948	849	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:16,250] [INFO] DFAST Taxonomy check result was written to GCF_021412585.1_ASM2141258v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:16,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:16,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:16,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference/checkm_data
[2024-01-24 13:46:16,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:16,299] [INFO] Task started: CheckM
[2024-01-24 13:46:16,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021412585.1_ASM2141258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021412585.1_ASM2141258v1_genomic.fna/checkm_input GCF_021412585.1_ASM2141258v1_genomic.fna/checkm_result
[2024-01-24 13:47:02,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:02,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,441] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:02,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:02,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021412585.1_ASM2141258v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:02,442] [INFO] Task started: Blastn
[2024-01-24 13:47:02,442] [INFO] Running command: blastn -query GCF_021412585.1_ASM2141258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge88e1fe9-d079-4fac-9e17-337452e6c339/dqc_reference/reference_markers_gtdb.fasta -out GCF_021412585.1_ASM2141258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:04,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:04,458] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:04,458] [INFO] Target genome list was writen to GCF_021412585.1_ASM2141258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:04,481] [INFO] Task started: fastANI
[2024-01-24 13:47:04,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee14b6d-95a6-4041-9d65-ac60c10e6aab/GCF_021412585.1_ASM2141258v1_genomic.fna.gz --refList GCF_021412585.1_ASM2141258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021412585.1_ASM2141258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:15,704] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:15,714] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:15,714] [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_003336675.1	s__Halomonas montanilacus	92.5478	1218	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545155.1	s__Halomonas chromatireducens	91.6975	1124	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129225.1	s__Halomonas sp007129225	89.7737	744	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339685.1	s__Halomonas sp003339685	89.6706	976	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	83.96	973	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002879615.1	s__Halomonas endophytica	83.546	934	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	82.8155	954	1601	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	82.713	957	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	82.2726	794	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553625.1	s__Halomonas sp003553625	82.0596	603	1601	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.58	0.84	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:15,716] [INFO] GTDB search result was written to GCF_021412585.1_ASM2141258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:15,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:15,720] [INFO] DFAST_QC result json was written to GCF_021412585.1_ASM2141258v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:15,721] [INFO] DFAST_QC completed!
[2024-01-24 13:47:15,721] [INFO] Total running time: 0h1m34s