[2024-01-24 14:19:19,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:19,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:19,117] [INFO] DQC Reference Directory: /var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference
[2024-01-24 14:19:20,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,661] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eced053-6685-4c12-8061-465863bc5c8d/GCF_004343255.1_ASM434325v1_genomic.fna.gz | prodigal -d GCF_004343255.1_ASM434325v1_genomic.fna/cds.fna -a GCF_004343255.1_ASM434325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:34,665] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:34,666] [INFO] Task started: HMMsearch
[2024-01-24 14:19:34,666] [INFO] Running command: hmmsearch --tblout GCF_004343255.1_ASM434325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference/reference_markers.hmm GCF_004343255.1_ASM434325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:34,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:34,959] [INFO] Found 6/6 markers.
[2024-01-24 14:19:35,010] [INFO] Query marker FASTA was written to GCF_004343255.1_ASM434325v1_genomic.fna/markers.fasta
[2024-01-24 14:19:35,014] [INFO] Task started: Blastn
[2024-01-24 14:19:35,014] [INFO] Running command: blastn -query GCF_004343255.1_ASM434325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference/reference_markers.fasta -out GCF_004343255.1_ASM434325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:35,674] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:35,678] [INFO] Selected 20 target genomes.
[2024-01-24 14:19:35,679] [INFO] Target genome list was writen to GCF_004343255.1_ASM434325v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:35,686] [INFO] Task started: fastANI
[2024-01-24 14:19:35,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eced053-6685-4c12-8061-465863bc5c8d/GCF_004343255.1_ASM434325v1_genomic.fna.gz --refList GCF_004343255.1_ASM434325v1_genomic.fna/target_genomes.txt --output GCF_004343255.1_ASM434325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:48,350] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:48,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:48,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:48,359] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:48,359] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:19:48,359] [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
Laceyella sacchari	strain=DSM 43356	GCA_004343255.1	37482	37482	type	True	100.0	1080	1083	95	inconclusive
Laceyella sediminis	strain=RHA1	GCA_003003125.1	573074	573074	type	True	95.1933	1000	1083	95	inconclusive
Thermoactinomyces daqus	strain=H-18	GCA_000763315.1	1329516	1329516	type	True	77.2887	145	1083	95	below_threshold
Thermoactinomyces mirandus	strain=AMNI-1	GCA_013868055.1	2756294	2756294	type	True	77.165	69	1083	95	below_threshold
Lihuaxuella thermophila	strain=DSM 46701	GCA_900110165.1	1173111	1173111	type	True	77.1219	125	1083	95	below_threshold
Thermoactinomyces vulgaris	strain=DSM 43016	GCA_003688725.1	2026	2026	type	True	76.7574	108	1083	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	76.6942	73	1083	95	below_threshold
Thermoactinomyces intermedius	strain=NRRL B-16979	GCA_013912365.1	2024	2024	type	True	76.5527	103	1083	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:48,361] [INFO] DFAST Taxonomy check result was written to GCF_004343255.1_ASM434325v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:48,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:48,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:48,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference/checkm_data
[2024-01-24 14:19:48,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:48,397] [INFO] Task started: CheckM
[2024-01-24 14:19:48,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004343255.1_ASM434325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004343255.1_ASM434325v1_genomic.fna/checkm_input GCF_004343255.1_ASM434325v1_genomic.fna/checkm_result
[2024-01-24 14:20:33,236] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:33,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:33,260] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:33,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:33,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004343255.1_ASM434325v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:33,262] [INFO] Task started: Blastn
[2024-01-24 14:20:33,262] [INFO] Running command: blastn -query GCF_004343255.1_ASM434325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge76b647a-4b78-4e03-85b5-436d96fba365/dqc_reference/reference_markers_gtdb.fasta -out GCF_004343255.1_ASM434325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:34,122] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:34,126] [INFO] Selected 22 target genomes.
[2024-01-24 14:20:34,126] [INFO] Target genome list was writen to GCF_004343255.1_ASM434325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:34,161] [INFO] Task started: fastANI
[2024-01-24 14:20:34,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eced053-6685-4c12-8061-465863bc5c8d/GCF_004343255.1_ASM434325v1_genomic.fna.gz --refList GCF_004343255.1_ASM434325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004343255.1_ASM434325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:47,059] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:47,074] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:47,074] [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_004343255.1	s__Laceyella sacchari	100.0	1080	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	96.84	96.83	0.94	0.94	3	conclusive
GCF_003003125.1	s__Laceyella sediminis	95.1919	1000	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	97.79	97.73	0.93	0.93	3	-
GCF_000763315.1	s__Thermoactinomyces_A daqus	77.2887	145	1083	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_013868055.1	s__Thermoactinomyces mirandus	77.1275	70	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110165.1	s__Lihuaxuella thermophila	77.1235	124	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Lihuaxuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856495.1	s__Staphylospora marina	76.7219	72	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688725.1	s__Thermoactinomyces vulgaris	76.7005	109	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces	95.0	98.49	95.03	0.97	0.93	17	-
GCF_003313465.1	s__Thermoflavimicrobium sp003313465	76.6209	51	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoflavimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:47,076] [INFO] GTDB search result was written to GCF_004343255.1_ASM434325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:47,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:47,080] [INFO] DFAST_QC result json was written to GCF_004343255.1_ASM434325v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:47,080] [INFO] DFAST_QC completed!
[2024-01-24 14:20:47,080] [INFO] Total running time: 0h1m28s