[2024-01-24 13:21:59,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:59,202] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:59,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference
[2024-01-24 13:22:00,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:00,460] [INFO] Task started: Prodigal
[2024-01-24 13:22:00,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg69213f21-de56-485c-8c3b-8f3ec0f8c636/GCF_004195885.1_ASM419588v1_genomic.fna.gz | prodigal -d GCF_004195885.1_ASM419588v1_genomic.fna/cds.fna -a GCF_004195885.1_ASM419588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:19,108] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:19,108] [INFO] Task started: HMMsearch
[2024-01-24 13:22:19,108] [INFO] Running command: hmmsearch --tblout GCF_004195885.1_ASM419588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference/reference_markers.hmm GCF_004195885.1_ASM419588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:19,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:19,527] [INFO] Found 6/6 markers.
[2024-01-24 13:22:19,580] [INFO] Query marker FASTA was written to GCF_004195885.1_ASM419588v1_genomic.fna/markers.fasta
[2024-01-24 13:22:19,580] [INFO] Task started: Blastn
[2024-01-24 13:22:19,581] [INFO] Running command: blastn -query GCF_004195885.1_ASM419588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference/reference_markers.fasta -out GCF_004195885.1_ASM419588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:20,934] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:20,937] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:20,937] [INFO] Target genome list was writen to GCF_004195885.1_ASM419588v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:20,944] [INFO] Task started: fastANI
[2024-01-24 13:22:20,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg69213f21-de56-485c-8c3b-8f3ec0f8c636/GCF_004195885.1_ASM419588v1_genomic.fna.gz --refList GCF_004195885.1_ASM419588v1_genomic.fna/target_genomes.txt --output GCF_004195885.1_ASM419588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:44,091] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:44,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:44,101] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:44,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:44,102] [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	99.1346	2186	2293	95	conclusive
Streptomyces albidoflavus	strain=DSM 40455	GCA_004195735.1	1886	1886	type	True	99.1343	2161	2293	95	conclusive
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	91.9835	1845	2293	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=JCM 4128	GCA_014648935.1	68040	1956	suspected-type	True	91.886	1852	2293	95	below_threshold
Streptomyces gougerotii	strain=NBRC 13043	GCA_011170145.1	53448	53448	suspected-type	True	91.8735	1875	2293	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=NBRC 13412	GCA_011170125.1	68040	1956	suspected-type	True	91.8398	1873	2293	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.8083	1281	2293	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.7231	998	2293	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.4484	1043	2293	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.2412	1334	2293	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.2129	1258	2293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,107] [INFO] DFAST Taxonomy check result was written to GCF_004195885.1_ASM419588v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:44,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:44,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:44,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference/checkm_data
[2024-01-24 13:22:44,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:44,177] [INFO] Task started: CheckM
[2024-01-24 13:22:44,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004195885.1_ASM419588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004195885.1_ASM419588v1_genomic.fna/checkm_input GCF_004195885.1_ASM419588v1_genomic.fna/checkm_result
[2024-01-24 13:24:13,259] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:13,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:13,286] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:13,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:13,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004195885.1_ASM419588v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:13,287] [INFO] Task started: Blastn
[2024-01-24 13:24:13,287] [INFO] Running command: blastn -query GCF_004195885.1_ASM419588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb191625d-6861-46cf-b862-c69adb43ec5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004195885.1_ASM419588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:15,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:15,530] [INFO] Selected 23 target genomes.
[2024-01-24 13:24:15,530] [INFO] Target genome list was writen to GCF_004195885.1_ASM419588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:15,583] [INFO] Task started: fastANI
[2024-01-24 13:24:15,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg69213f21-de56-485c-8c3b-8f3ec0f8c636/GCF_004195885.1_ASM419588v1_genomic.fna.gz --refList GCF_004195885.1_ASM419588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004195885.1_ASM419588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:59,749] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:59,771] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:59,772] [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	99.1346	2186	2293	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	91.8397	1873	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	-
GCF_014655295.1	s__Streptomyces fumanus	82.0618	1354	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939385.1	s__Streptomyces sp002939385	82.0036	1311	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCA_004010275.1	s__Streptomyces huasconensis	81.829	1244	2293	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	81.811	1377	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_014650895.1	s__Streptomyces omiyaensis	81.759	1375	2293	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	81.7501	1359	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_003671715.1	s__Streptomyces sp003671715	81.7184	1325	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_004784465.1	s__Streptomyces griseoluteus	81.7049	1223	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_008704515.1	s__Streptomyces viridosporus	81.6972	1297	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_000720835.1	s__Streptomyces achromogenes	81.6216	1266	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	81.5995	1340	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_008042145.1	s__Streptomyces sp008042145	81.5976	1288	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042045.1	s__Streptomyces sp008042045	81.5805	1295	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642695.1	s__Streptomyces chilikensis	81.3939	1183	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716675.1	s__Streptomyces alboflavus	81.3732	1374	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_003112515.1	s__Streptomyces fragilis	81.3666	1196	2293	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	81.3515	1318	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_014649115.1	s__Streptomyces eurythermus	81.3468	1354	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_009650765.1	s__Streptomyces sp003259585	81.3229	1278	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.79	98.74	0.95	0.93	5	-
GCF_001509485.1	s__Streptomyces sp001509485	81.1321	1167	2293	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364195.1	s__Streptomyces sp013364195	81.0817	1215	2293	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 13:24:59,773] [INFO] GTDB search result was written to GCF_004195885.1_ASM419588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:59,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:59,778] [INFO] DFAST_QC result json was written to GCF_004195885.1_ASM419588v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:59,778] [INFO] DFAST_QC completed!
[2024-01-24 13:24:59,778] [INFO] Total running time: 0h3m1s