[2024-01-24 11:05:24,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,249] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,249] [INFO] DQC Reference Directory: /var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference
[2024-01-24 11:05:25,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,875] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7a9885d-cd6d-46e3-95f0-9f70427b858c/GCF_014650435.1_ASM1465043v1_genomic.fna.gz | prodigal -d GCF_014650435.1_ASM1465043v1_genomic.fna/cds.fna -a GCF_014650435.1_ASM1465043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:50,391] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:50,392] [INFO] Task started: HMMsearch
[2024-01-24 11:05:50,392] [INFO] Running command: hmmsearch --tblout GCF_014650435.1_ASM1465043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference/reference_markers.hmm GCF_014650435.1_ASM1465043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:50,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:50,801] [INFO] Found 6/6 markers.
[2024-01-24 11:05:50,873] [INFO] Query marker FASTA was written to GCF_014650435.1_ASM1465043v1_genomic.fna/markers.fasta
[2024-01-24 11:05:50,873] [INFO] Task started: Blastn
[2024-01-24 11:05:50,873] [INFO] Running command: blastn -query GCF_014650435.1_ASM1465043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference/reference_markers.fasta -out GCF_014650435.1_ASM1465043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:52,202] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:52,205] [INFO] Selected 22 target genomes.
[2024-01-24 11:05:52,205] [INFO] Target genome list was writen to GCF_014650435.1_ASM1465043v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:52,213] [INFO] Task started: fastANI
[2024-01-24 11:05:52,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7a9885d-cd6d-46e3-95f0-9f70427b858c/GCF_014650435.1_ASM1465043v1_genomic.fna.gz --refList GCF_014650435.1_ASM1465043v1_genomic.fna/target_genomes.txt --output GCF_014650435.1_ASM1465043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:33,548] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:33,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:33,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:33,571] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:33,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:33,571] [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 tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	100.0	2910	2912	95	conclusive
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	94.3458	2259	2912	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	94.0023	2339	2912	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	93.8764	2271	2912	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	93.1861	2079	2912	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	92.0819	2100	2912	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	89.0571	1928	2912	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.8895	1912	2912	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.949	1546	2912	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.4975	1774	2912	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.2448	1465	2912	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.2036	1817	2912	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.5446	1592	2912	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	84.5007	1540	2912	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	82.0397	1353	2912	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	81.9973	1383	2912	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	81.9851	1368	2912	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.7427	1198	2912	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.4345	966	2912	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	76.7533	525	2912	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.6015	597	2912	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	76.545	546	2912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:33,573] [INFO] DFAST Taxonomy check result was written to GCF_014650435.1_ASM1465043v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:33,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:33,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:33,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference/checkm_data
[2024-01-24 11:06:33,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:33,653] [INFO] Task started: CheckM
[2024-01-24 11:06:33,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650435.1_ASM1465043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650435.1_ASM1465043v1_genomic.fna/checkm_input GCF_014650435.1_ASM1465043v1_genomic.fna/checkm_result
[2024-01-24 11:08:31,319] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:31,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:31,350] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:31,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:31,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650435.1_ASM1465043v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:31,351] [INFO] Task started: Blastn
[2024-01-24 11:08:31,351] [INFO] Running command: blastn -query GCF_014650435.1_ASM1465043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge166da9f-a3c6-4754-806b-271227e17c88/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650435.1_ASM1465043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:33,501] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:33,505] [INFO] Selected 19 target genomes.
[2024-01-24 11:08:33,505] [INFO] Target genome list was writen to GCF_014650435.1_ASM1465043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:33,537] [INFO] Task started: fastANI
[2024-01-24 11:08:33,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7a9885d-cd6d-46e3-95f0-9f70427b858c/GCF_014650435.1_ASM1465043v1_genomic.fna.gz --refList GCF_014650435.1_ASM1465043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650435.1_ASM1465043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:09:14,048] [INFO] Task succeeded: fastANI
[2024-01-24 11:09:14,063] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:09:14,064] [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_014650435.1	s__Streptomyces tendae	100.0	2910	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	conclusive
GCF_002939385.1	s__Streptomyces sp002939385	94.0763	2152	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_003112595.1	s__Streptomyces rubrogriseus	93.9838	2342	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCA_000720845.1	s__Streptomyces sp000720845	93.9775	2249	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651155.1	s__Streptomyces anthocyanicus	93.837	2276	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCF_003369795.1	s__Streptomyces sp003369795	93.5353	2127	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	93.2104	2076	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	92.6649	2208	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_000772045.1	s__Streptomyces sp000772045	92.6508	2182	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_003112575.1	s__Streptomyces ardesiacus	92.0873	2100	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_004364245.1	s__Streptomyces sp004364245	92.0004	2051	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	89.9535	2018	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCA_000696115.1	s__Streptomyces olindensis	85.4465	1760	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205055.1	s__Streptomyces luteogriseus	85.2555	1777	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_000761215.1	s__Streptomyces glaucescens	85.1104	1669	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	84.832	1638	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_010548275.1	s__Streptomyces sp010548275	83.2677	1618	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	79.662	1215	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	78.4319	968	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:09:14,066] [INFO] GTDB search result was written to GCF_014650435.1_ASM1465043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:09:14,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:09:14,071] [INFO] DFAST_QC result json was written to GCF_014650435.1_ASM1465043v1_genomic.fna/dqc_result.json
[2024-01-24 11:09:14,071] [INFO] DFAST_QC completed!
[2024-01-24 11:09:14,071] [INFO] Total running time: 0h3m50s