[2024-01-25 17:47:05,758] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:05,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:05,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference
[2024-01-25 17:47:06,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:06,937] [INFO] Task started: Prodigal
[2024-01-25 17:47:06,937] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdde11ee-3a44-4424-96a6-f164def67ff0/GCF_031454155.1_ASM3145415v1_genomic.fna.gz | prodigal -d GCF_031454155.1_ASM3145415v1_genomic.fna/cds.fna -a GCF_031454155.1_ASM3145415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:16,940] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:16,940] [INFO] Task started: HMMsearch
[2024-01-25 17:47:16,940] [INFO] Running command: hmmsearch --tblout GCF_031454155.1_ASM3145415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference/reference_markers.hmm GCF_031454155.1_ASM3145415v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:17,153] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:17,155] [INFO] Found 6/6 markers.
[2024-01-25 17:47:17,188] [INFO] Query marker FASTA was written to GCF_031454155.1_ASM3145415v1_genomic.fna/markers.fasta
[2024-01-25 17:47:17,188] [INFO] Task started: Blastn
[2024-01-25 17:47:17,188] [INFO] Running command: blastn -query GCF_031454155.1_ASM3145415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference/reference_markers.fasta -out GCF_031454155.1_ASM3145415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:17,730] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:17,733] [INFO] Selected 17 target genomes.
[2024-01-25 17:47:17,733] [INFO] Target genome list was writen to GCF_031454155.1_ASM3145415v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:17,741] [INFO] Task started: fastANI
[2024-01-25 17:47:17,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdde11ee-3a44-4424-96a6-f164def67ff0/GCF_031454155.1_ASM3145415v1_genomic.fna.gz --refList GCF_031454155.1_ASM3145415v1_genomic.fna/target_genomes.txt --output GCF_031454155.1_ASM3145415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:28,519] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:28,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:28,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:28,527] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:47:28,527] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:47:28,528] [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
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	78.4294	396	1207	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	77.106	139	1207	95	below_threshold
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	77.0914	141	1207	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	76.9254	172	1207	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	76.7578	161	1207	95	below_threshold
Melghirimyces algeriensis	strain=DSM 45474	GCA_900182565.1	910412	910412	type	True	76.7535	98	1207	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_900156615.1	714067	714067	type	True	76.7441	163	1207	95	below_threshold
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	76.6489	96	1207	95	below_threshold
Melghirimyces thermohalophilus	strain=DSM 45514	GCA_900102685.1	1236220	1236220	type	True	76.5287	133	1207	95	below_threshold
Marininema halotolerans	strain=DSM 45789	GCA_900116235.1	1155944	1155944	type	True	76.4179	56	1207	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.2547	89	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:28,529] [INFO] DFAST Taxonomy check result was written to GCF_031454155.1_ASM3145415v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:28,529] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:28,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:28,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference/checkm_data
[2024-01-25 17:47:28,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:28,568] [INFO] Task started: CheckM
[2024-01-25 17:47:28,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031454155.1_ASM3145415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031454155.1_ASM3145415v1_genomic.fna/checkm_input GCF_031454155.1_ASM3145415v1_genomic.fna/checkm_result
[2024-01-25 17:48:00,299] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:00,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:00,316] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:00,316] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:00,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031454155.1_ASM3145415v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:00,317] [INFO] Task started: Blastn
[2024-01-25 17:48:00,317] [INFO] Running command: blastn -query GCF_031454155.1_ASM3145415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3bd2004-8586-4375-b9a1-9ef3f9ccc120/dqc_reference/reference_markers_gtdb.fasta -out GCF_031454155.1_ASM3145415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:01,136] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:01,139] [INFO] Selected 18 target genomes.
[2024-01-25 17:48:01,139] [INFO] Target genome list was writen to GCF_031454155.1_ASM3145415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:01,151] [INFO] Task started: fastANI
[2024-01-25 17:48:01,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdde11ee-3a44-4424-96a6-f164def67ff0/GCF_031454155.1_ASM3145415v1_genomic.fna.gz --refList GCF_031454155.1_ASM3145415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031454155.1_ASM3145415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:15,362] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:15,370] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:48:15,370] [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_003046315.1	s__Desmospora activa	78.4191	397	1207	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_014641195.1	s__Marinithermofilum abyssi	77.106	139	1207	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_002245355.1	s__Paludifilum halophilum	77.0914	141	1207	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_003054245.1	s__Melghirimyces profundicolus	76.9524	169	1207	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	76.7535	98	1207	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_013282215.1	s__Kroppenstedtia eburnea	76.7445	162	1207	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_013265585.1	s__Kroppenstedtia_A pulmonis	76.6489	96	1207	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_900102685.1	s__Melghirimyces thermohalophilus	76.543	132	1207	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_900116235.1	s__Marininema halotolerans	76.4179	56	1207	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_003001905.1	s__Planifilum fimeticola	76.2357	90	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:15,372] [INFO] GTDB search result was written to GCF_031454155.1_ASM3145415v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:15,373] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:15,376] [INFO] DFAST_QC result json was written to GCF_031454155.1_ASM3145415v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:15,376] [INFO] DFAST_QC completed!
[2024-01-25 17:48:15,376] [INFO] Total running time: 0h1m10s