[2024-01-24 11:35:11,159] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference
[2024-01-24 11:35:12,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,586] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,587] [INFO] Running command: gunzip -c /var/lib/cwl/stga2e00026-c8ee-4913-9340-d9fb8c0dd12e/GCF_018326425.1_ASM1832642v1_genomic.fna.gz | prodigal -d GCF_018326425.1_ASM1832642v1_genomic.fna/cds.fna -a GCF_018326425.1_ASM1832642v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:23,269] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:23,269] [INFO] Task started: HMMsearch
[2024-01-24 11:35:23,269] [INFO] Running command: hmmsearch --tblout GCF_018326425.1_ASM1832642v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference/reference_markers.hmm GCF_018326425.1_ASM1832642v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:23,529] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:23,530] [INFO] Found 6/6 markers.
[2024-01-24 11:35:23,556] [INFO] Query marker FASTA was written to GCF_018326425.1_ASM1832642v1_genomic.fna/markers.fasta
[2024-01-24 11:35:23,556] [INFO] Task started: Blastn
[2024-01-24 11:35:23,557] [INFO] Running command: blastn -query GCF_018326425.1_ASM1832642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference/reference_markers.fasta -out GCF_018326425.1_ASM1832642v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:24,190] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:24,193] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:24,193] [INFO] Target genome list was writen to GCF_018326425.1_ASM1832642v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:24,202] [INFO] Task started: fastANI
[2024-01-24 11:35:24,202] [INFO] Running command: fastANI --query /var/lib/cwl/stga2e00026-c8ee-4913-9340-d9fb8c0dd12e/GCF_018326425.1_ASM1832642v1_genomic.fna.gz --refList GCF_018326425.1_ASM1832642v1_genomic.fna/target_genomes.txt --output GCF_018326425.1_ASM1832642v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:37,919] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:37,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:37,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:37,930] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:37,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:37,930] [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	100.0	1063	1065	95	conclusive
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	79.0844	150	1065	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	78.4756	80	1065	95	below_threshold
Planifilum fulgidum	strain=DSM 44945	GCA_900113175.1	201973	201973	type	True	77.0513	101	1065	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.8485	109	1065	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	76.7973	103	1065	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.6717	62	1065	95	below_threshold
Kroppenstedtia guangzhouensis	strain=CGMCC 1.12404	GCA_014637345.1	1274356	1274356	type	True	76.5208	61	1065	95	below_threshold
Thermoactinomyces intermedius	strain=NRRL B-16979	GCA_013912365.1	2024	2024	type	True	76.3823	61	1065	95	below_threshold
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	76.2642	73	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:37,932] [INFO] DFAST Taxonomy check result was written to GCF_018326425.1_ASM1832642v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:37,933] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:37,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:37,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference/checkm_data
[2024-01-24 11:35:37,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:37,971] [INFO] Task started: CheckM
[2024-01-24 11:35:37,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018326425.1_ASM1832642v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018326425.1_ASM1832642v1_genomic.fna/checkm_input GCF_018326425.1_ASM1832642v1_genomic.fna/checkm_result
[2024-01-24 11:36:14,186] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:14,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,211] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:14,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:14,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018326425.1_ASM1832642v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:14,212] [INFO] Task started: Blastn
[2024-01-24 11:36:14,213] [INFO] Running command: blastn -query GCF_018326425.1_ASM1832642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg617131d7-2b77-44cc-932f-024e4a59406e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018326425.1_ASM1832642v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:15,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:15,100] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:15,100] [INFO] Target genome list was writen to GCF_018326425.1_ASM1832642v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:15,135] [INFO] Task started: fastANI
[2024-01-24 11:36:15,135] [INFO] Running command: fastANI --query /var/lib/cwl/stga2e00026-c8ee-4913-9340-d9fb8c0dd12e/GCF_018326425.1_ASM1832642v1_genomic.fna.gz --refList GCF_018326425.1_ASM1832642v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018326425.1_ASM1832642v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:28,068] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:28,081] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:28,081] [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	100.0	1063	1065	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__JIR-001;g__Polycladomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014641195.1	s__Marinithermofilum abyssi	79.0257	152	1065	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	78.2197	78	1065	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113175.1	s__Planifilum fulgidum	77.0307	101	1065	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_003001905.1	s__Planifilum fimeticola	76.8485	109	1065	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	76.8197	101	1065	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	76.6717	62	1065	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_014637345.1	s__Kroppenstedtia guangzhouensis	76.4829	61	1065	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245355.1	s__Paludifilum halophilum	76.2888	72	1065	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Paludifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:28,083] [INFO] GTDB search result was written to GCF_018326425.1_ASM1832642v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:28,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:28,087] [INFO] DFAST_QC result json was written to GCF_018326425.1_ASM1832642v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:28,088] [INFO] DFAST_QC completed!
[2024-01-24 11:36:28,088] [INFO] Total running time: 0h1m17s