[2024-01-24 12:16:08,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,056] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference
[2024-01-24 12:16:09,403] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,404] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d78e8d7-abef-4e2e-b743-243f1df39298/GCF_014637345.1_ASM1463734v1_genomic.fna.gz | prodigal -d GCF_014637345.1_ASM1463734v1_genomic.fna/cds.fna -a GCF_014637345.1_ASM1463734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:20,492] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:20,492] [INFO] Task started: HMMsearch
[2024-01-24 12:16:20,493] [INFO] Running command: hmmsearch --tblout GCF_014637345.1_ASM1463734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference/reference_markers.hmm GCF_014637345.1_ASM1463734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:20,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:20,750] [INFO] Found 6/6 markers.
[2024-01-24 12:16:20,785] [INFO] Query marker FASTA was written to GCF_014637345.1_ASM1463734v1_genomic.fna/markers.fasta
[2024-01-24 12:16:20,785] [INFO] Task started: Blastn
[2024-01-24 12:16:20,785] [INFO] Running command: blastn -query GCF_014637345.1_ASM1463734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference/reference_markers.fasta -out GCF_014637345.1_ASM1463734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:21,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:21,406] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:21,406] [INFO] Target genome list was writen to GCF_014637345.1_ASM1463734v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:21,412] [INFO] Task started: fastANI
[2024-01-24 12:16:21,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d78e8d7-abef-4e2e-b743-243f1df39298/GCF_014637345.1_ASM1463734v1_genomic.fna.gz --refList GCF_014637345.1_ASM1463734v1_genomic.fna/target_genomes.txt --output GCF_014637345.1_ASM1463734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:28,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:28,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:28,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:28,851] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:28,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:28,852] [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
Kroppenstedtia guangzhouensis	strain=CGMCC 1.12404	GCA_014637345.1	1274356	1274356	type	True	100.0	1155	1157	95	conclusive
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	88.9304	925	1157	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_900156615.1	714067	714067	type	True	88.8716	912	1157	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	77.4999	240	1157	95	below_threshold
Melghirimyces algeriensis	strain=DSM 45474	GCA_900182565.1	910412	910412	type	True	77.1672	141	1157	95	below_threshold
Melghirimyces thermohalophilus	strain=DSM 45514	GCA_900102685.1	1236220	1236220	type	True	77.0952	199	1157	95	below_threshold
Polycladomyces abyssicola	strain=JIR-001	GCA_018326425.1	1125966	1125966	type	True	76.3116	61	1157	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.0503	96	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:28,853] [INFO] DFAST Taxonomy check result was written to GCF_014637345.1_ASM1463734v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:28,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:28,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:28,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference/checkm_data
[2024-01-24 12:16:28,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:28,895] [INFO] Task started: CheckM
[2024-01-24 12:16:28,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637345.1_ASM1463734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637345.1_ASM1463734v1_genomic.fna/checkm_input GCF_014637345.1_ASM1463734v1_genomic.fna/checkm_result
[2024-01-24 12:17:05,961] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:05,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:05,984] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:05,984] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:05,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637345.1_ASM1463734v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:05,985] [INFO] Task started: Blastn
[2024-01-24 12:17:05,985] [INFO] Running command: blastn -query GCF_014637345.1_ASM1463734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c7e5d4-82ea-41be-bc55-65e051f53310/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637345.1_ASM1463734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:06,852] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:06,856] [INFO] Selected 12 target genomes.
[2024-01-24 12:17:06,856] [INFO] Target genome list was writen to GCF_014637345.1_ASM1463734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:06,865] [INFO] Task started: fastANI
[2024-01-24 12:17:06,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d78e8d7-abef-4e2e-b743-243f1df39298/GCF_014637345.1_ASM1463734v1_genomic.fna.gz --refList GCF_014637345.1_ASM1463734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637345.1_ASM1463734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:14,623] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:14,642] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:14,643] [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_014637345.1	s__Kroppenstedtia guangzhouensis	100.0	1155	1157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013282215.1	s__Kroppenstedtia eburnea	88.9304	925	1157	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_003054245.1	s__Melghirimyces profundicolus	77.5047	239	1157	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_900182565.1	s__Melghirimyces algeriensis	77.1889	139	1157	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_900102685.1	s__Melghirimyces thermohalophilus	77.0952	199	1157	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_900106775.1	s__Marininema mesophilum	76.5518	56	1157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marininema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113175.1	s__Planifilum fulgidum	76.3132	98	1157	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_018326425.1	s__Polycladomyces abyssicola	76.3116	61	1157	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_003001905.1	s__Planifilum fimeticola	76.0503	96	1157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:14,645] [INFO] GTDB search result was written to GCF_014637345.1_ASM1463734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:14,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:14,650] [INFO] DFAST_QC result json was written to GCF_014637345.1_ASM1463734v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:14,650] [INFO] DFAST_QC completed!
[2024-01-24 12:17:14,651] [INFO] Total running time: 0h1m7s