[2024-01-24 13:17:11,679] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference
[2024-01-24 13:17:12,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,900] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,900] [INFO] Running command: gunzip -c /var/lib/cwl/stg27ba242c-2998-421a-a7a6-1bbee5306fa0/GCF_003428925.1_ASM342892v1_genomic.fna.gz | prodigal -d GCF_003428925.1_ASM342892v1_genomic.fna/cds.fna -a GCF_003428925.1_ASM342892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,465] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,465] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,466] [INFO] Running command: hmmsearch --tblout GCF_003428925.1_ASM342892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference/reference_markers.hmm GCF_003428925.1_ASM342892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,807] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,809] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,863] [INFO] Query marker FASTA was written to GCF_003428925.1_ASM342892v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,863] [INFO] Task started: Blastn
[2024-01-24 13:17:33,863] [INFO] Running command: blastn -query GCF_003428925.1_ASM342892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference/reference_markers.fasta -out GCF_003428925.1_ASM342892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:35,160] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:35,164] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:35,164] [INFO] Target genome list was writen to GCF_003428925.1_ASM342892v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:35,199] [INFO] Task started: fastANI
[2024-01-24 13:17:35,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ba242c-2998-421a-a7a6-1bbee5306fa0/GCF_003428925.1_ASM342892v1_genomic.fna.gz --refList GCF_003428925.1_ASM342892v1_genomic.fna/target_genomes.txt --output GCF_003428925.1_ASM342892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:57,221] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:57,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:57,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:57,232] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:57,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:57,233] [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 albidoflavus	strain=NRRL B-1271	GCA_000719955.1	1886	1886	type	True	96.0558	2052	2406	95	conclusive
Streptomyces albidoflavus	strain=DSM 40455	GCA_004195735.1	1886	1886	type	True	96.0109	2050	2406	95	conclusive
Streptomyces gougerotii	strain=NBRC 13043	GCA_011170145.1	53448	53448	suspected-type	True	91.8628	1889	2406	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	91.844	1837	2406	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=NBRC 13412	GCA_011170125.1	68040	1956	suspected-type	True	91.7946	1901	2406	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=JCM 4128	GCA_014648935.1	68040	1956	suspected-type	True	91.7242	1868	2406	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.9066	1250	2406	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.9004	1284	2406	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.7574	1009	2406	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.3457	1293	2406	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.1007	1284	2406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:57,235] [INFO] DFAST Taxonomy check result was written to GCF_003428925.1_ASM342892v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:57,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:57,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:57,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference/checkm_data
[2024-01-24 13:17:57,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:57,308] [INFO] Task started: CheckM
[2024-01-24 13:17:57,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003428925.1_ASM342892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003428925.1_ASM342892v1_genomic.fna/checkm_input GCF_003428925.1_ASM342892v1_genomic.fna/checkm_result
[2024-01-24 13:19:25,234] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:25,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,257] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:25,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:25,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003428925.1_ASM342892v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:25,259] [INFO] Task started: Blastn
[2024-01-24 13:19:25,259] [INFO] Running command: blastn -query GCF_003428925.1_ASM342892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7971bfab-53c0-4f9c-995a-104034b80f58/dqc_reference/reference_markers_gtdb.fasta -out GCF_003428925.1_ASM342892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,465] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:27,466] [INFO] Target genome list was writen to GCF_003428925.1_ASM342892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:27,518] [INFO] Task started: fastANI
[2024-01-24 13:19:27,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ba242c-2998-421a-a7a6-1bbee5306fa0/GCF_003428925.1_ASM342892v1_genomic.fna.gz --refList GCF_003428925.1_ASM342892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003428925.1_ASM342892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:09,524] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:09,545] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:09,545] [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_000719955.1	s__Streptomyces albidoflavus	96.0444	2053	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	95.93	0.92	0.84	100	conclusive
GCF_011170125.1	s__Streptomyces diastaticus	91.8148	1897	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	-
GCA_003268675.1	s__Streptomyces bacillaris	82.136	1414	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
GCF_002939385.1	s__Streptomyces sp002939385	82.0288	1307	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCA_012396115.1	s__Streptomyces somaliensis	81.8616	851	2406	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	81.8058	1379	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_016905445.1	s__Streptomyces sp016905445	81.7746	1249	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004784465.1	s__Streptomyces griseoluteus	81.7696	1220	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCA_004010275.1	s__Streptomyces huasconensis	81.765	1242	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	81.7165	1384	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_003671715.1	s__Streptomyces sp003671715	81.6906	1315	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_007679425.1	s__Streptomyces incarnatus_A	81.6084	1222	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_008042045.1	s__Streptomyces sp008042045	81.6017	1312	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860525.1	s__Streptomyces rubradiris	81.5396	1347	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_000720835.1	s__Streptomyces achromogenes	81.4647	1256	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	81.4426	1338	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_001418415.1	s__Streptomyces hirsutus	81.4333	1131	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.60	97.60	0.78	0.78	2	-
GCF_009650765.1	s__Streptomyces sp003259585	81.4024	1287	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.79	98.74	0.95	0.93	5	-
GCF_000716675.1	s__Streptomyces alboflavus	81.3799	1367	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_900236475.1	s__Streptomyces chartreusis_D	81.2675	1326	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	81.2628	1280	2406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_013364195.1	s__Streptomyces sp013364195	81.2344	1189	2406	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 13:20:09,547] [INFO] GTDB search result was written to GCF_003428925.1_ASM342892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:09,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:09,552] [INFO] DFAST_QC result json was written to GCF_003428925.1_ASM342892v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:09,552] [INFO] DFAST_QC completed!
[2024-01-24 13:20:09,552] [INFO] Total running time: 0h2m58s