[2024-01-24 10:56:34,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference
[2024-01-24 10:56:36,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,717] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbb4aa3e-477e-43d2-aec4-e26c717bb454/GCF_014649315.1_ASM1464931v1_genomic.fna.gz | prodigal -d GCF_014649315.1_ASM1464931v1_genomic.fna/cds.fna -a GCF_014649315.1_ASM1464931v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:56:59,823] [INFO] Task succeeded: Prodigal
[2024-01-24 10:56:59,823] [INFO] Task started: HMMsearch
[2024-01-24 10:56:59,824] [INFO] Running command: hmmsearch --tblout GCF_014649315.1_ASM1464931v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference/reference_markers.hmm GCF_014649315.1_ASM1464931v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:00,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:00,163] [INFO] Found 6/6 markers.
[2024-01-24 10:57:00,223] [INFO] Query marker FASTA was written to GCF_014649315.1_ASM1464931v1_genomic.fna/markers.fasta
[2024-01-24 10:57:00,224] [INFO] Task started: Blastn
[2024-01-24 10:57:00,224] [INFO] Running command: blastn -query GCF_014649315.1_ASM1464931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference/reference_markers.fasta -out GCF_014649315.1_ASM1464931v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:01,525] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:01,529] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:01,529] [INFO] Target genome list was writen to GCF_014649315.1_ASM1464931v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:01,535] [INFO] Task started: fastANI
[2024-01-24 10:57:01,536] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb4aa3e-477e-43d2-aec4-e26c717bb454/GCF_014649315.1_ASM1464931v1_genomic.fna.gz --refList GCF_014649315.1_ASM1464931v1_genomic.fna/target_genomes.txt --output GCF_014649315.1_ASM1464931v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:38,357] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:38,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:38,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:38,379] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:38,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:38,379] [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
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	100.0	2618	2620	95	conclusive
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	99.9932	2604	2620	95	conclusive
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	91.6182	2120	2620	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	91.6131	2117	2620	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	91.127	2050	2620	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	91.1	2046	2620	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	89.3994	1898	2620	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	89.3456	1926	2620	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	89.2258	1895	2620	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	88.8096	1802	2620	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	88.7348	1499	2620	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.4125	1810	2620	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.3307	1821	2620	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	86.1686	1769	2620	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.8948	1788	2620	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.865	1528	2620	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.8344	1573	2620	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:38,381] [INFO] DFAST Taxonomy check result was written to GCF_014649315.1_ASM1464931v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:38,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:38,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:38,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference/checkm_data
[2024-01-24 10:57:38,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:38,456] [INFO] Task started: CheckM
[2024-01-24 10:57:38,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649315.1_ASM1464931v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649315.1_ASM1464931v1_genomic.fna/checkm_input GCF_014649315.1_ASM1464931v1_genomic.fna/checkm_result
[2024-01-24 10:59:41,482] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:41,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:41,514] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:41,515] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:41,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649315.1_ASM1464931v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:41,515] [INFO] Task started: Blastn
[2024-01-24 10:59:41,516] [INFO] Running command: blastn -query GCF_014649315.1_ASM1464931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96700ced-68ea-476e-a463-9c1088bcc5b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649315.1_ASM1464931v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:43,594] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:43,604] [INFO] Selected 12 target genomes.
[2024-01-24 10:59:43,604] [INFO] Target genome list was writen to GCF_014649315.1_ASM1464931v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:43,614] [INFO] Task started: fastANI
[2024-01-24 10:59:43,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb4aa3e-477e-43d2-aec4-e26c717bb454/GCF_014649315.1_ASM1464931v1_genomic.fna.gz --refList GCF_014649315.1_ASM1464931v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649315.1_ASM1464931v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:11,078] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:11,100] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:11,100] [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_006782915.1	s__Streptomyces calvus	99.9776	2584	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	conclusive
GCF_007829875.1	s__Streptomyces capillispiralis	91.6182	2116	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014650015.1	s__Streptomyces griseoloalbus	91.2199	2053	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	-
GCF_019049255.1	s__Streptomyces sp019049255	89.8724	2009	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	89.7798	1981	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	89.7219	1927	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	89.5503	1979	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312835.1	s__Streptomyces marokkonensis	89.4981	1903	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665435.1	s__Streptomyces fungicidicus_A	89.4892	1933	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.42	0.93	0.90	4	-
GCF_014203535.1	s__Streptomyces griseostramineus	89.3318	1928	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCA_000696115.1	s__Streptomyces olindensis	86.3951	1786	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237655.1	s__Streptomyces sp002237655	86.256	1836	2620	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:11,102] [INFO] GTDB search result was written to GCF_014649315.1_ASM1464931v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:11,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:11,107] [INFO] DFAST_QC result json was written to GCF_014649315.1_ASM1464931v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:11,107] [INFO] DFAST_QC completed!
[2024-01-24 11:00:11,107] [INFO] Total running time: 0h3m36s