[2024-01-24 13:32:41,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference
[2024-01-24 13:32:42,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,637] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,637] [INFO] Running command: gunzip -c /var/lib/cwl/stge411a3d8-e6e0-45f3-84e5-a86812eab792/GCF_030433435.1_ASM3043343v1_genomic.fna.gz | prodigal -d GCF_030433435.1_ASM3043343v1_genomic.fna/cds.fna -a GCF_030433435.1_ASM3043343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:53,400] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:53,401] [INFO] Task started: HMMsearch
[2024-01-24 13:32:53,401] [INFO] Running command: hmmsearch --tblout GCF_030433435.1_ASM3043343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference/reference_markers.hmm GCF_030433435.1_ASM3043343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:53,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:53,622] [INFO] Found 6/6 markers.
[2024-01-24 13:32:53,651] [INFO] Query marker FASTA was written to GCF_030433435.1_ASM3043343v1_genomic.fna/markers.fasta
[2024-01-24 13:32:53,651] [INFO] Task started: Blastn
[2024-01-24 13:32:53,651] [INFO] Running command: blastn -query GCF_030433435.1_ASM3043343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference/reference_markers.fasta -out GCF_030433435.1_ASM3043343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:54,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:54,277] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:54,277] [INFO] Target genome list was writen to GCF_030433435.1_ASM3043343v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:54,284] [INFO] Task started: fastANI
[2024-01-24 13:32:54,284] [INFO] Running command: fastANI --query /var/lib/cwl/stge411a3d8-e6e0-45f3-84e5-a86812eab792/GCF_030433435.1_ASM3043343v1_genomic.fna.gz --refList GCF_030433435.1_ASM3043343v1_genomic.fna/target_genomes.txt --output GCF_030433435.1_ASM3043343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:03,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:03,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:03,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:03,250] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:03,250] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:03,250] [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
Polycladomyces abyssicola	strain=JIR-001	GCA_018326425.1	1125966	1125966	type	True	91.1848	934	1093	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	78.303	138	1093	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	76.7942	86	1093	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.6657	119	1093	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	76.6649	101	1093	95	below_threshold
Thermoactinomyces daqus	strain=H-18	GCA_000763315.1	1329516	1329516	type	True	76.6573	79	1093	95	below_threshold
Thermoactinomyces intermedius	strain=NRRL B-16979	GCA_013912365.1	2024	2024	type	True	76.5898	55	1093	95	below_threshold
Planifilum fulgidum	strain=DSM 44945	GCA_900113175.1	201973	201973	type	True	76.4628	111	1093	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.4555	66	1093	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	76.3596	72	1093	95	below_threshold
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	76.1742	71	1093	95	below_threshold
Melghirimyces thermohalophilus	strain=DSM 45514	GCA_900102685.1	1236220	1236220	type	True	75.9354	77	1093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:03,252] [INFO] DFAST Taxonomy check result was written to GCF_030433435.1_ASM3043343v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:03,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:03,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:03,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference/checkm_data
[2024-01-24 13:33:03,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:03,288] [INFO] Task started: CheckM
[2024-01-24 13:33:03,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030433435.1_ASM3043343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030433435.1_ASM3043343v1_genomic.fna/checkm_input GCF_030433435.1_ASM3043343v1_genomic.fna/checkm_result
[2024-01-24 13:33:39,043] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:39,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:39,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:39,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:39,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030433435.1_ASM3043343v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:39,064] [INFO] Task started: Blastn
[2024-01-24 13:33:39,064] [INFO] Running command: blastn -query GCF_030433435.1_ASM3043343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg795893b3-036e-4f2a-91fc-8131c466f4eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_030433435.1_ASM3043343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:39,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:39,852] [INFO] Selected 18 target genomes.
[2024-01-24 13:33:39,853] [INFO] Target genome list was writen to GCF_030433435.1_ASM3043343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:39,931] [INFO] Task started: fastANI
[2024-01-24 13:33:39,931] [INFO] Running command: fastANI --query /var/lib/cwl/stge411a3d8-e6e0-45f3-84e5-a86812eab792/GCF_030433435.1_ASM3043343v1_genomic.fna.gz --refList GCF_030433435.1_ASM3043343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030433435.1_ASM3043343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:50,557] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:50,566] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:33:50,566] [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_018326425.1	s__Polycladomyces abyssicola	91.1848	934	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__JIR-001;g__Polycladomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641195.1	s__Marinithermofilum abyssi	78.3313	137	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marinithermofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856495.1	s__Staphylospora marina	76.7942	86	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001905.1	s__Planifilum fimeticola	76.6657	119	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054245.1	s__Melghirimyces profundicolus	76.6649	101	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763315.1	s__Thermoactinomyces_A daqus	76.6329	78	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces_A	95.0	99.52	99.22	0.92	0.88	5	-
GCF_003046315.1	s__Desmospora activa	76.4808	65	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Desmospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113175.1	s__Planifilum fulgidum	76.4467	112	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	99.34	99.26	0.97	0.97	3	-
GCF_013282215.1	s__Kroppenstedtia eburnea	76.3897	73	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	99.43	98.85	0.98	0.95	3	-
GCF_002245355.1	s__Paludifilum halophilum	76.1742	71	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Paludifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102685.1	s__Melghirimyces thermohalophilus	75.9354	77	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:50,568] [INFO] GTDB search result was written to GCF_030433435.1_ASM3043343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:50,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:50,572] [INFO] DFAST_QC result json was written to GCF_030433435.1_ASM3043343v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:50,572] [INFO] DFAST_QC completed!
[2024-01-24 13:33:50,572] [INFO] Total running time: 0h1m9s