[2024-01-24 13:18:26,158] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,160] [INFO] DQC Reference Directory: /var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference
[2024-01-24 13:18:27,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,549] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg714aa391-d8d5-4fc3-a3ab-f16a5e061ee7/GCF_014141525.1_ASM1414152v1_genomic.fna.gz | prodigal -d GCF_014141525.1_ASM1414152v1_genomic.fna/cds.fna -a GCF_014141525.1_ASM1414152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:42,272] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:42,272] [INFO] Task started: HMMsearch
[2024-01-24 13:18:42,272] [INFO] Running command: hmmsearch --tblout GCF_014141525.1_ASM1414152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference/reference_markers.hmm GCF_014141525.1_ASM1414152v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:42,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:42,614] [INFO] Found 6/6 markers.
[2024-01-24 13:18:42,670] [INFO] Query marker FASTA was written to GCF_014141525.1_ASM1414152v1_genomic.fna/markers.fasta
[2024-01-24 13:18:42,670] [INFO] Task started: Blastn
[2024-01-24 13:18:42,671] [INFO] Running command: blastn -query GCF_014141525.1_ASM1414152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference/reference_markers.fasta -out GCF_014141525.1_ASM1414152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:44,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:44,078] [INFO] Selected 22 target genomes.
[2024-01-24 13:18:44,079] [INFO] Target genome list was writen to GCF_014141525.1_ASM1414152v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:44,098] [INFO] Task started: fastANI
[2024-01-24 13:18:44,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg714aa391-d8d5-4fc3-a3ab-f16a5e061ee7/GCF_014141525.1_ASM1414152v1_genomic.fna.gz --refList GCF_014141525.1_ASM1414152v1_genomic.fna/target_genomes.txt --output GCF_014141525.1_ASM1414152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:12,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:12,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:12,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:12,084] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:12,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:12,085] [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 calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	100.0	1302	1327	95	conclusive
Streptomyces alkaliphilus	strain=DSM 42118	GCA_014141535.1	1472722	1472722	type	True	91.5401	751	1327	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	81.1517	608	1327	95	below_threshold
Streptomyces aidingensis	strain=CGMCC 4.5739	GCA_900112355.1	910347	910347	type	True	80.7825	705	1327	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	80.605	582	1327	95	below_threshold
Streptomyces bohaiensis	strain=11A07	GCA_012033785.1	1431344	1431344	type	True	80.6033	557	1327	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	80.54	616	1327	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	80.5056	639	1327	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	80.4717	516	1327	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.327	519	1327	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	80.0834	601	1327	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	79.9708	621	1327	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	79.9482	643	1327	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	79.9011	592	1327	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	79.8074	549	1327	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.6216	613	1327	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.561	598	1327	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.5553	565	1327	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.5269	497	1327	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	79.4035	569	1327	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.3709	598	1327	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	78.7595	521	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:12,092] [INFO] DFAST Taxonomy check result was written to GCF_014141525.1_ASM1414152v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:12,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:12,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:12,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference/checkm_data
[2024-01-24 13:19:12,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:12,161] [INFO] Task started: CheckM
[2024-01-24 13:19:12,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014141525.1_ASM1414152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014141525.1_ASM1414152v1_genomic.fna/checkm_input GCF_014141525.1_ASM1414152v1_genomic.fna/checkm_result
[2024-01-24 13:20:03,353] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:03,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:03,385] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:03,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:03,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014141525.1_ASM1414152v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:03,387] [INFO] Task started: Blastn
[2024-01-24 13:20:03,387] [INFO] Running command: blastn -query GCF_014141525.1_ASM1414152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf717a134-82a9-4a31-b0c9-9f8f937436e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014141525.1_ASM1414152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:05,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:05,525] [INFO] Selected 29 target genomes.
[2024-01-24 13:20:05,525] [INFO] Target genome list was writen to GCF_014141525.1_ASM1414152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:05,592] [INFO] Task started: fastANI
[2024-01-24 13:20:05,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg714aa391-d8d5-4fc3-a3ab-f16a5e061ee7/GCF_014141525.1_ASM1414152v1_genomic.fna.gz --refList GCF_014141525.1_ASM1414152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014141525.1_ASM1414152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:42,880] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:42,914] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:42,914] [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_011421595.1	s__Streptomyces sp011421595	81.1486	696	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004305975.1	s__Streptomyces otsuchiensis	81.1478	608	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_009709575.1	s__Streptomyces taklimakanensis	80.9059	637	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012033735.1	s__Streptomyces lonarensis	80.6679	576	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	80.6663	625	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_012033785.1	s__Streptomyces bohaiensis	80.6074	557	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	80.5952	610	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_012034385.1	s__Streptomyces sp012034385	80.5183	569	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	80.503	613	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097205.2	s__Streptomyces alkaliterrae	80.4641	517	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_000993785.3	s__Streptomyces xiamenensis	80.4468	612	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	97.97	0.94	0.91	3	-
GCF_004348315.1	s__Streptomyces sp004348315	80.1004	609	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	80.0593	590	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696235.1	s__Streptomyces triticirhizae	80.0532	604	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_014083985.1	s__SCUT-3 sp014083985	80.0347	569	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	80.0056	617	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426325.1	s__Streptomyces sp000426325	79.9326	564	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.50	96.50	0.91	0.91	2	-
GCF_008632955.1	s__Streptomyces sp000527195	79.7687	568	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.14	95.85	0.89	0.84	5	-
GCF_007595705.1	s__Streptomyces sp007595705	79.7603	595	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	79.7086	591	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000719135.1	s__Streptomyces avicenniae	79.6566	563	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000444875.1	s__Streptomyces collinus_A	79.5831	569	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.10	97.10	0.84	0.84	2	-
GCF_000719555.1	s__Streptomyces sp000719555	79.4407	593	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	79.3848	580	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514215.1	s__Streptomyces bungoensis	79.3734	616	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	79.3276	603	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	79.2443	629	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_000701325.1	s__Streptomyces sp000701325	79.1732	563	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005085.2	s__Streptomyces humi	78.8925	577	1327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.38	96.38	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:42,916] [INFO] GTDB search result was written to GCF_014141525.1_ASM1414152v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:42,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:42,922] [INFO] DFAST_QC result json was written to GCF_014141525.1_ASM1414152v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:42,922] [INFO] DFAST_QC completed!
[2024-01-24 13:20:42,922] [INFO] Total running time: 0h2m17s