[2024-01-25 19:07:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:35,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:35,568] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference
[2024-01-25 19:07:36,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:36,713] [INFO] Task started: Prodigal
[2024-01-25 19:07:36,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg840e3f49-54f6-4477-a942-c0405f3efd80/GCF_014141535.1_ASM1414153v1_genomic.fna.gz | prodigal -d GCF_014141535.1_ASM1414153v1_genomic.fna/cds.fna -a GCF_014141535.1_ASM1414153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:49,266] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:49,266] [INFO] Task started: HMMsearch
[2024-01-25 19:07:49,266] [INFO] Running command: hmmsearch --tblout GCF_014141535.1_ASM1414153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference/reference_markers.hmm GCF_014141535.1_ASM1414153v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:49,577] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:49,578] [INFO] Found 6/6 markers.
[2024-01-25 19:07:49,624] [INFO] Query marker FASTA was written to GCF_014141535.1_ASM1414153v1_genomic.fna/markers.fasta
[2024-01-25 19:07:49,625] [INFO] Task started: Blastn
[2024-01-25 19:07:49,625] [INFO] Running command: blastn -query GCF_014141535.1_ASM1414153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference/reference_markers.fasta -out GCF_014141535.1_ASM1414153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:50,906] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:50,908] [INFO] Selected 25 target genomes.
[2024-01-25 19:07:50,909] [INFO] Target genome list was writen to GCF_014141535.1_ASM1414153v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:50,927] [INFO] Task started: fastANI
[2024-01-25 19:07:50,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg840e3f49-54f6-4477-a942-c0405f3efd80/GCF_014141535.1_ASM1414153v1_genomic.fna.gz --refList GCF_014141535.1_ASM1414153v1_genomic.fna/target_genomes.txt --output GCF_014141535.1_ASM1414153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:19,540] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:19,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:19,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:19,556] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:08:19,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:19,556] [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 alkaliphilus	strain=DSM 42118	GCA_014141535.1	1472722	1472722	type	True	100.0	1088	1110	95	conclusive
Streptomyces calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	91.5729	775	1110	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	81.074	544	1110	95	below_threshold
Streptomyces aidingensis	strain=CGMCC 4.5739	GCA_900112355.1	910347	910347	type	True	80.7747	605	1110	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	80.6497	519	1110	95	below_threshold
Streptomyces bohaiensis	strain=11A07	GCA_012033785.1	1431344	1431344	type	True	80.588	506	1110	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	80.5873	442	1110	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	80.5751	563	1110	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	80.5081	564	1110	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	80.494	560	1110	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.4425	467	1110	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	80.2238	567	1110	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	80.0841	497	1110	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	79.8076	560	1110	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	79.7572	545	1110	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.6991	437	1110	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.6656	535	1110	95	below_threshold
Streptomyces catenulae	strain=NRRL B-2342	GCA_000718015.1	66875	66875	type	True	79.5837	465	1110	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	79.5679	514	1110	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	79.5638	466	1110	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.5193	437	1110	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.5014	505	1110	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.4311	510	1110	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	79.3648	487	1110	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	79.1951	491	1110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:19,558] [INFO] DFAST Taxonomy check result was written to GCF_014141535.1_ASM1414153v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:19,558] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:19,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:19,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference/checkm_data
[2024-01-25 19:08:19,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:19,617] [INFO] Task started: CheckM
[2024-01-25 19:08:19,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014141535.1_ASM1414153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014141535.1_ASM1414153v1_genomic.fna/checkm_input GCF_014141535.1_ASM1414153v1_genomic.fna/checkm_result
[2024-01-25 19:09:04,410] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:04,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:04,426] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:04,426] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:04,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014141535.1_ASM1414153v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:04,427] [INFO] Task started: Blastn
[2024-01-25 19:09:04,427] [INFO] Running command: blastn -query GCF_014141535.1_ASM1414153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb6a9487-4d2d-46d3-bd11-e21d1f882e95/dqc_reference/reference_markers_gtdb.fasta -out GCF_014141535.1_ASM1414153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:06,501] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:06,504] [INFO] Selected 34 target genomes.
[2024-01-25 19:09:06,504] [INFO] Target genome list was writen to GCF_014141535.1_ASM1414153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:06,528] [INFO] Task started: fastANI
[2024-01-25 19:09:06,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg840e3f49-54f6-4477-a942-c0405f3efd80/GCF_014141535.1_ASM1414153v1_genomic.fna.gz --refList GCF_014141535.1_ASM1414153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014141535.1_ASM1414153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:47,918] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:47,938] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:09:47,938] [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	81.2206	614	1110	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	81.081	544	1110	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	81.0304	557	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112355.1	s__Streptomyces aidingensis	80.8093	602	1110	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	80.6392	536	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	80.6158	559	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_012033785.1	s__Streptomyces bohaiensis	80.5772	507	1110	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	80.5595	444	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_017114865.1	s__Streptomyces verrucosisporus	80.4923	565	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_002982015.1	s__Streptomyces sp002982015	80.1679	475	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779715.1	s__Streptomyces chumphonensis	80.1444	490	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	80.1142	526	1110	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	80.0262	520	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	79.988	517	1110	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_000426325.1	s__Streptomyces sp000426325	79.8921	487	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.50	96.50	0.91	0.91	2	-
GCF_003696235.1	s__Streptomyces triticirhizae	79.8746	531	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	79.8169	559	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	79.8132	528	1110	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	79.7871	523	1110	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	79.7832	483	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548465.1	s__Streptomyces sp010548465	79.6845	460	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	79.6542	508	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718015.1	s__Streptomyces catenulae	79.6403	460	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003519485.1	s__Streptomyces sp003519485	79.5214	344	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	79.5101	538	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_016916835.1	s__Streptomyces bryophytorum	79.3987	483	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900091855.1	s__Streptomyces sp900091855	79.3755	431	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000701325.1	s__Streptomyces sp000701325	79.3699	455	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107965.1	s__Streptomyces yanglinensis	79.2342	487	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355155.1	s__Streptomyces armeniacus	79.2223	498	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	79.169	505	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_000719335.1	s__Streptomyces sp000719335	79.0769	507	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646055.1	s__Streptomyces_A tyrosinilyticus	79.011	457	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514205.1	s__Streptomyces griseoruber	78.8347	510	1110	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:47,942] [INFO] GTDB search result was written to GCF_014141535.1_ASM1414153v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:47,943] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:47,948] [INFO] DFAST_QC result json was written to GCF_014141535.1_ASM1414153v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:47,948] [INFO] DFAST_QC completed!
[2024-01-25 19:09:47,948] [INFO] Total running time: 0h2m12s