[2024-01-24 13:32:35,157] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,159] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,159] [INFO] DQC Reference Directory: /var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference
[2024-01-24 13:32:36,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,588] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,588] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4b41934-d223-4ca6-a456-b0b5e5296d01/GCF_002245355.1_ASM224535v1_genomic.fna.gz | prodigal -d GCF_002245355.1_ASM224535v1_genomic.fna/cds.fna -a GCF_002245355.1_ASM224535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:47,924] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:47,925] [INFO] Task started: HMMsearch
[2024-01-24 13:32:47,925] [INFO] Running command: hmmsearch --tblout GCF_002245355.1_ASM224535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference/reference_markers.hmm GCF_002245355.1_ASM224535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:48,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:48,307] [INFO] Found 6/6 markers.
[2024-01-24 13:32:48,345] [INFO] Query marker FASTA was written to GCF_002245355.1_ASM224535v1_genomic.fna/markers.fasta
[2024-01-24 13:32:48,345] [INFO] Task started: Blastn
[2024-01-24 13:32:48,346] [INFO] Running command: blastn -query GCF_002245355.1_ASM224535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference/reference_markers.fasta -out GCF_002245355.1_ASM224535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,997] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,000] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:49,001] [INFO] Target genome list was writen to GCF_002245355.1_ASM224535v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:49,008] [INFO] Task started: fastANI
[2024-01-24 13:32:49,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4b41934-d223-4ca6-a456-b0b5e5296d01/GCF_002245355.1_ASM224535v1_genomic.fna.gz --refList GCF_002245355.1_ASM224535v1_genomic.fna/target_genomes.txt --output GCF_002245355.1_ASM224535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:04,419] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:04,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:04,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:04,429] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:04,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:04,430] [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
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	100.0	1220	1221	95	conclusive
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	77.4192	156	1221	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	77.24	192	1221	95	below_threshold
Melghirimyces thermohalophilus	strain=DSM 45514	GCA_900102685.1	1236220	1236220	type	True	76.9755	149	1221	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.9678	143	1221	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	76.9416	174	1221	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_900156615.1	714067	714067	type	True	76.9198	175	1221	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.5283	80	1221	95	below_threshold
Planifilum fulgidum	strain=DSM 44945	GCA_900113175.1	201973	201973	type	True	76.2329	95	1221	95	below_threshold
Polycladomyces abyssicola	strain=JIR-001	GCA_018326425.1	1125966	1125966	type	True	76.016	74	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:04,432] [INFO] DFAST Taxonomy check result was written to GCF_002245355.1_ASM224535v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:04,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:04,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:04,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference/checkm_data
[2024-01-24 13:33:04,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:04,478] [INFO] Task started: CheckM
[2024-01-24 13:33:04,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002245355.1_ASM224535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002245355.1_ASM224535v1_genomic.fna/checkm_input GCF_002245355.1_ASM224535v1_genomic.fna/checkm_result
[2024-01-24 13:33:42,850] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:42,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:42,881] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:42,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:42,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002245355.1_ASM224535v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:42,882] [INFO] Task started: Blastn
[2024-01-24 13:33:42,882] [INFO] Running command: blastn -query GCF_002245355.1_ASM224535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge29f9f18-1f2c-4674-afca-e0350deadec1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002245355.1_ASM224535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:43,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:43,729] [INFO] Selected 22 target genomes.
[2024-01-24 13:33:43,729] [INFO] Target genome list was writen to GCF_002245355.1_ASM224535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:43,758] [INFO] Task started: fastANI
[2024-01-24 13:33:43,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4b41934-d223-4ca6-a456-b0b5e5296d01/GCF_002245355.1_ASM224535v1_genomic.fna.gz --refList GCF_002245355.1_ASM224535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002245355.1_ASM224535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:58,052] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:58,065] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:58,065] [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_002245355.1	s__Paludifilum halophilum	100.0	1220	1221	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Paludifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013265585.1	s__Kroppenstedtia_A pulmonis	77.4016	157	1221	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054245.1	s__Melghirimyces profundicolus	77.2253	193	1221	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	76.9929	148	1221	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_003046315.1	s__Desmospora activa	76.9678	143	1221	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_013282215.1	s__Kroppenstedtia eburnea	76.9017	178	1221	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_003001905.1	s__Planifilum fimeticola	76.5278	79	1221	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_900113175.1	s__Planifilum fulgidum	76.2264	94	1221	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	76.016	74	1221	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__JIR-001;g__Polycladomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:58,067] [INFO] GTDB search result was written to GCF_002245355.1_ASM224535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:58,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:58,070] [INFO] DFAST_QC result json was written to GCF_002245355.1_ASM224535v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:58,070] [INFO] DFAST_QC completed!
[2024-01-24 13:33:58,070] [INFO] Total running time: 0h1m23s